Your attachments still aren't through, but I can let you in on some unrelated stuff going on in your form:
In a screen reader, the "select one" will not get read out if the reader has a Forms Mode (as the two big Windows screen readers do). If you need only one selected, make them radio buttons. (checkbox practically BEGS "check none or more"! while radio buttons say "you must choose one and only one", like the old radio buttons in cars in the 70's. remember those?)
<input type="checkbox" name="checkbox3" value="checkbox" />
<label for="HCA"><a href="#" class="check">Text</a> </label>
I have recently discovered (the hard way) that having an anchor wrapped around the label text inside the label seems to remove the benefit of being able to click on the label to select the input (one of the touted benefits of explicit linking with the "for" attribute) in all browsers except Firefox (for whatever reason).
This hasn't stopped me from using anchors in labels for when I needed a focus point or help text, but be aware of it. I found Opera, Saffy, Chrome, and IE6 and 7 let you click either the label or the input, but clicking the label did not select the input except in FF.
<ul> <input type="checkbox" name="checkbox4" value="checkbox" />
This part is illegal. Are you sure this is what you have?
While I don't personally like lists in forms, you can have them in there legally, but legally the only valid child of a ul is a li. When people make listed forms, they put all the form controls in a li because they must.
The li has all the same abilities of a div, and can contain just about anything. I looked at your link and they don't mix lists with divs... they just use jQuery to add a bunch of divs for rounded corners.
And it looks like jQuery just is there to make a "parent selector" (something CSS is sorely lacking!). I'm sure there's a css way to do it still, but right now I think we need to backtrack and figure out where these lists are coming from, because they way you've got them now, they're illegal (and likely screwing with one or more browsers despite their attempts at covering up our errors, lawlz).
You don't need to use a ul to get checkboxes indented. You just put them (and their label) in a box like a div and throw some left padding on the div or something.
For that matter, <div class="single-field"> looks like it may need to be a fieldset. You can put fieldsets in fieldsets, and you can put divs in fieldsets.
I'll see if I can bug someone about your attachments getting approved if they aren't approved today, but so long as you have invalid code it may be moot... we've gotta fix that first. Then figure out what you need to get the indenting you want.