This can happen with custom modules and skins. I have a page on my site that exibits this behavior.
http://www.jupiterchristian.org/Academics/Library/tabid/65/Default.aspx
If you follow one of the links in the repository module it will perform a postback and the underlying page layout will break in several ways:
1) the side menu's image gets cut off.
2) the aggragator tabs get smashed and a hover class appears even though I have not defined one for the tabs.
3) the site is designed for 1024x768 screen res but if you view it at a higher resolution and do the postback, the page is no longer centered but aligned to the left.
And it looks a lot better now than when I first discovered the problem! I don't have a lot of answers for you and could not find many myself even though some great people here advised me on some things to look at. I was able to do some damage control by tweaking certain css classes and also changing some width values of certain div tags.
This postback and css issue, if that is the issue, caught me off guard. My div based layout was working great until I added a module that needed to do postbacks.
Play around with your skin file, especially classes/selectors associated with your menu(s). I tried removing all modules except the one that needed to perform the postback, but that didn't help. Still, I would try it just to eliminate the possibility. Someone with more javascript knowledge may be able to help you see if any things being injected at the top of the page that is invalid and maybe causing the issue.
I'd like to hear back if you find an answer to your problem. It may motivate me to get back into my skin and give it another try.
Paul