Hmm, indeed, there are some problems.
First of all, the reason why initially IE was making a mess of all but the main page is because the first page has a doctype specified but other pages don't. You should add <!DOCTYPE HTML> as the topmost line to all of the pages.
Secondly, it seems like you've overwritten one menu's gradient image with other menu's gradient background. FF and Chrome use native CSS gradients, they don't need the background image, that's why you only see this in IE. To be absolutely sure that this does not happen, store all menu files in separate folders such as /topmenu/ and /sidemenu/. Please read this article to make sure your menus work even in pages in subfolders:
http://kb.blumentals.net/kb/index.php?V ... ntryID=134
My suggestion is to remove current menus and related css and regenerate them in separate folders, that should do the trick as long as page doctype is set. And that way you don't need to copy them to a common css file manually.
If you have more trouble, let me know or contact customer support, we'll help you.