It is always a little hard to deal with questions like this that deal with php since the php writes out html for the page source and we cannot see the php itself. However, here are a few things that need checking.
First, there are quite a few code errors, and some of them can easily cause some of the problems you are looking at. For example there are tags that are not closed. Certain tags in certain locations will not generate problems when this is done, but some of your div's have that issue and that usually does throw things off.
Second, on some pages you have scripts that are not placed in either the head or body, even outside the html tags. This is never correct as far as I know and may be causing problems as well either because they are causing issues being where they are or because they are not doing what you planned for them at all on some pages.
I would start by correcting the code errors and see what happens.