Hi,
You are using flexbox on nearly everything (including the body) and is pretty much overkill. However the problem is that you are using the most advanced CSS on the most out of date a page. 
There is no doctype on your page so you switch into quirks mode and flexbox suffers as a result.
Add a doctype to the top of the page:
<!DOCTYPE HTML>
I believe that will fix your issues.
As an aside note that In future it would have been better if you had constructed the page from your files and pasted them in a working manner like this:
<!DOCTYPE HTML>
<html>
<head>
<title>Title</title>
<style>
* {
direction: rtl
}
@font-face {
src: url("fonts/sans.woff");
font-family: "sans"
}
a {
text-decoration: none;
color: inherit
}
a:visited {
color: inherit
}
i {
color: #F7F8DE
}
a, h1, h2, h3, h4, h5, h6, li, p, span {
font-family: "sans", tahoma;
color: #757D75
}
h1 {
font-size: 2.3em
}
h2 {
font-size: 2em
}
h3 {
font-size: 1.8em
}
h4 {
font-size: 1.6em
}
h5 {
font-size: 1.4em
}
h6 {
font-size: 1.2em
}
body {
background: url("../images/main-bg.jpg") no-repeat center center;
background-size: cover;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column
}
input[type="checkbox"] {
border-radius: 3px;
border-color: #F7F8DE;
width: 50px !important
}
table {
border-collapse: collapse;
font-family: "sans", tahoma;
line-height: 2;
color: white
}
table td, table th {
box-shadow: inset 0 -1px rgba(0, 0, 0, 0.25), inset 0 1px rgba(0, 0, 0, 0.25)
}
table th {
font-weight: normal;
-webkit-font-smoothing: antialiased;
padding: 1em;
color: rgba(0, 0, 0, 0.45);
text-shadow: 0 0 1px rgba(0, 0, 0, 0.1);
font-size: 1em
}
table td {
color: #f7f7f7;
padding: 0.7em 1em 0.7em 1.15em;
text-shadow: 0 0 1px rgba(255, 255, 255, 0.1);
font-size: 0.8em
}
table td div {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
justify-content: center
}
table tr {
-webkit-transition: background 0.3s, box-shadow 0.3s;
-moz-transition: background 0.3s, box-shadow 0.3s;
transition: background 0.3s, box-shadow 0.3s
}
table tr:hover {
background: rgba(0, 0, 0, 0.1)
}
.next {
transition: background-color 0.3s;
padding-right: 2%;
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
margin-left: 35%;
background-color: #9b59b6;
align-items: center
}
.next:hover {
cursor: pointer
}
.next input {
border: none;
background: none;
color: #F7F8DE;
font-family: "sans", tahoma
}
.previous {
transition: background-color 0.3s;
padding-left: 2%;
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
direction: ltr;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
background-color: #8e44ad;
align-items: center
}
.previous:hover {
cursor: pointer
}
.previous input {
border: none;
background: none;
color: #F7F8DE;
font-family: "sans", tahoma
}
input[type=checkbox]:not(old), input[type=radio]:not(old) {
display: none
}
input[type=checkbox]:not(old)+label, input[type=radio]:not(old)+label {
display: inline-block;
text-align: center
}
input[type=checkbox]:not(old)+label>span, input[type=radio]:not(old)+label>span {
display: inline-block;
width: 1.5em;
height: 1.5em;
background: white;
background-image: -moz-linear-gradient(#f0f0f0, #e0e0e0);
background-image: -ms-linear-gradient(#f0f0f0, #e0e0e0);
background-image: -o-linear-gradient(#f0f0f0, #e0e0e0);
background-image: -webkit-linear-gradient(#f0f0f0, #e0e0e0);
background-image: linear-gradient(#f0f0f0, #e0e0e0);
vertical-align: bottom
}
input[type=checkbox]:not(old):checked+label>span, input[type=radio]:not(old):checked+label>span {
background-image: -moz-linear-gradient(#e0e0e0, #f0f0f0);
background-image: -ms-linear-gradient(#e0e0e0, #f0f0f0);
background-image: -o-linear-gradient(#e0e0e0, #f0f0f0);
background-image: -webkit-linear-gradient(#e0e0e0, #f0f0f0);
background-image: linear-gradient(#e0e0e0, #f0f0f0)
}
input[type=checkbox]:not(old):checked+label>span:before {
content: '✓';
width: 1em;
color: #f1c40f;
font-size: 1.5em;
line-height: 1em;
font-weight: bold;
text-align: center
}
#cpPage {
padding: 50px;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
align-items: center
}
#cpPage .note {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
align-items: center;
padding: 7px 20px;
margin-bottom: 50px;
background-color: #4DAF7C
}
#cpPage .note i {
color: #F7F8DE
}
#cpPage .note span {
color: #F7F8DE;
margin-right: 15px
}
#cpPage .completeProfile form {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column
}
#cpPage .completeProfile form select[name="department"] {
overflow: scroll;
flex-basis: 40px;
padding: 5px 15px;
margin-bottom: 15px;
border: 1px solid #C0C0C0;
font-family: "sans", tahoma;
color: #757D75
}
#cpPage .completeProfile form input {
flex-basis: 40px;
padding: 5px 15px;
margin-bottom: 15px;
border: 1px solid #C0C0C0;
font-family: "sans", tahoma;
transition: border-color 0.2s
}
#cpPage .completeProfile form input:focus {
border-color: #26A65B
}
#cpPage .completeProfile form input[type="submit"] {
background-color: #264348;
color: #F7F8DE;
-webkit-transition: background-color 0.3s;
-moz-transition: background-color 0.3s
}
#cpPage .completeProfile form input[type="submit"]:hover {
background-color: #049372;
color: #F7F8DE
}
#dashboard {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
padding: 30px;
box-sizing: border-box
}
#dashboard #sidebar {
padding: 20px;
box-sizing: border-box;
background-color: #34495e;
color: #F7F8DE;
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
flex-basis: content;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column
}
#dashboard #sidebar .sidebarHeader {
align-items: center;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
border-bottom: 1px solid #bdc3c7;
padding-bottom: 10px
}
#dashboard #sidebar .sidebarHeader figure {
-webkit-box-flex: 3;
-webkit-flex: 3;
-ms-flex: 3;
flex: 3;
border: 3px solid #bdc3c7
}
#dashboard #sidebar .sidebarHeader h4 {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
color: #F7F8DE;
font-size: 1em;
text-align: center
}
#dashboard #sidebar .sidebarContent ul {
list-style: none;
padding-right: 0;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
justify-content: space-between
}
#dashboard #sidebar .sidebarContent ul li {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
align-items: center;
transition: background-color 0.3s;
margin-bottom: 15px;
padding: 2px 5px
}
#dashboard #sidebar .sidebarContent ul li:hover {
background-color: rgba(255, 255, 255, 0.3)
}
#dashboard #sidebar .sidebarContent a {
color: #F7F8DE;
font-size: 0.9em;
margin-right: 7px
}
#dashboard #sidebar .sidebarContent i {
color: #F7F8DE;
border-left: 1px solid #bdc3c7;
padding-left: 6px
}
#dashboard #sidebar .sidebarFooter {
border-top: 1px solid #bdc3c7;
padding-top: 15px;
text-align: center
}
#dashboard #sidebar .sidebarFooter a {
color: #F7F8DE;
font-family: tahoma;
font-size: 12px
}
#dashboard #body {
background-color: #FBFBFB;
border: 1px solid #757D75;
margin-right: 5%;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
align-items: center;
-webkit-box-flex: 3;
-webkit-flex: 3;
-ms-flex: 3;
flex: 3
}
#dashboard #body #modules {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
align-items: center;
padding: 30px 60px;
-webkit-box-flex: 3;
-webkit-flex: 3;
-ms-flex: 3;
flex: 3
}
#dashboard #body #modules #firstStep {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column
}
#dashboard #body #modules .note {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
align-items: center;
padding: 10px 25px;
margin-bottom: 30px;
background-color: #27ae60
}
#dashboard #body #modules .note span {
font: 13px/2.2 "sans", tahoma;
color: #F7F8DE;
margin-right: 1%
}
#dashboard #body #modules .note span {
flex: 17
}
#dashboard #body #modules .note i {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1
}
#dashboard #body #modules .department {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
align-items: center;
-webkit-box-flex: 3;
-webkit-flex: 3;
-ms-flex: 3;
flex: 3
}
#dashboard #body #modules .department span {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
font: bold 12px "sans", tahoma;
flex: 0.5;
margin: 20px auto
}
#dashboard #body #modules .department .step1Form {
flex: 3;
width: 100%;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
align-items: center
}
#dashboard #body #modules .department .step1Form select {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column;
border: 1px solid 1px solid #95A5A6;
width: 40%
}
#dashboard #body #modules .department .step1Form select option {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
font: 12px/20px "sans", tahoma;
color: #757D75
}
#dashboard #body #modules .department .step1Form select option:checked, #dashboard #body #modules .department .step1Form select option:hover {
background-color: #16A085 !important;
color: #F7F8DE
}
#dashboard #body #modules .department .step1Form input[type="submit"] {
margin-top: 20px;
background-color: #16A085;
font: 14px "sans";
color: #F7F8DE;
flex-basis: 40px;
padding: 5px 15px;
margin-bottom: 15px;
border: 1px solid #C0C0C0;
transition: background-color 0.3s
}
#dashboard #body #modules .department .step1Form input[type="submit"]:hover {
cursor: pointer
}
#dashboard #body footer {
background-color: #5D8CAE;
font: 13px tahoma;
padding: 10px 30px;
box-sizing: border-box;
width: 100%;
flex: 0.3;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row
}
#dashboard #body footer .copyright {
-webkit-box-flex: 1;
-webkit-flex: 1;
-ms-flex: 1;
flex: 1;
color: #F7F8DE
}
#dashboard #body footer .version {
color: #F7F8DE;
flex: 0.2
}
#dashboard #step2 {
flex: 1;
align-items: center;
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: column
}
#dashboard #step2 .note {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
align-items: center;
padding: 10px 25px;
margin-bottom: 30px;
background-color: #0eac51
}
#dashboard #step2 .note span {
font: 13px/2.2 "sans", tahoma;
color: #F7F8DE;
margin-right: 1%
}
#dashboard #step2 table {
background-color: #336ca6
}
#dashboard #step2 #navigation {
display: -webkit-flex;
display: -ms-flex;
display: -webkit-box;
display: flex;
flex-direction: row;
margin-top: 3%
}
body {
background: none;
background-color: #EEEEEE;
}
</style>
</head>
<body>
<div id="dashboard">
<div id="sidebar">
<div class="sidebarHeader">
<figure> عکس </figure>
<h4> heading</h4>
</div>
<div class="sidebarContent">
<ul>
<li> <i class="fa fa-key"> </i> <a href="#"> تغییر رمز عبور </a> </li>
<li> <i class="fa fa-question-circle-o"> </i> <a href="#"> راهنمای کار با سایت </a> </li>
<li> <i class="fa fa-smile-o"> </i> <a href="#"> معرفی به دوستان </a> </li>
<li> <i class="fa fa-sign-out"> </i> <a href="#"> خروج </a> </li>
</ul>
</div>
<div class="sidebarFooter"> <a href="#"> درباره سازندگان </a> </div>
</div>
<div id="body">
<div id="modules">
<div id="firstStep">
<div class="note"> <i class="fa fa-exclamation-circle fa-2x"></i> <span> اطلاعات زیر را وارد کنید و مرحله به مرحله پیش بروید. در پایان یک برنامه ی پیشنهادی برای ترم پیش رو خواهید داشت.
در حال حاضر این برنامه برای دانشگاه صنعتی شاهرود و ترم نخست 95-96 در دسترس میباشد. </span> </div>
<div class="department"> <span> دانشکده هایی که مایل به انتخاب دروس از آنها هستید را انتخاب کنید: </span>
<form action="#" method="post" class="step1Form">
<select multiple>
<option value="computer"> مهندسی کامپیوتر و فناوری اطلاعات </option>
<option value="electric"> مهندسی برق </option>
<option value="mechanic"> مهندسی مکانیک </option>
<option value="chemistry"> مهندسی شیمی </option>
<option value="civil"> مهندسی عمران </option>
<option value="mathematic"> علوم ریاضی </option>
<option value="architecture"> مهندسی معماری </option>
</select>
<input type="submit" value="بزن بریم!" class="step1Button">
</form>
</div>
</div>
<div id="step2">
<div class="note"> <i class="fa fa-book fa-2x"> </i> <span> در لیست زیر درسهای ارائه شده ی دانشکده ی های انتخاب شده وجود دارد، درسهای موردنظرتان را انتخاب کنید. </span> </div>
<form action="#" method="post">
<table class="step2Table">
<tr>
<th> انتخاب </th>
<th> نام درس </th>
<th> دانشکده </th>
</tr>
<tr>
<td><div>
<input type="checkbox" id="flatCheckBox">
<label for="flatCheckBox"><span><span></span></span></label>
</div></td>
<td> برنامه نویسی </td>
<td> کامپیوتر و فناوری اطلاعات </td>
</tr>
</table>
<div id="navigation">
<div class="next"> <i class="fa fa-arrow-right"> </i>
<input type="submit" value="مرحله بعدی">
</div>
<div class="previous"> <i class="fa fa-arrow-left"></i>
<input type="button" name="#" value="مرحله قبلی">
</div>
</div>
</form>
</div>
</div>
<footer>
<div class="copyright" > © طراحی و توسعه از فلان تیم </div>
<div class="version"> برنامه فلان، نسخه 0.1 </div>
</footer>
</div>
</div>
</body>
As it was I had to spend 15 minutes downloading, concatenating and constructing the page before I could test if my guess was right 