first I like to point out that your CSS3 isnt very “older” CSS3 browser friendly… .you may want t go back an add -webkit and -moz version of your rules for increased support of older browsers.
The box shadow property IS NOT inherited. Which makes me wonder if you declared it in a rule that also affected your sections. a good way to test this is to go back and DELETE the box-shadow declaration where you used it and declare it in ITS OWN separate rule:
Because you have box-shadow on each .container div, you get the effect you are seeing on the home page. You’d be better off to rethink your layout, and use a single .container div on the home page and within that have those modules with a different class name.