This is by far the most bizarre thing I've come across in my experience of web development. When I click a link to page.php, it takes me to page.php and the layout is fine (surprisingly not the bizarre bit). However, if I then refresh that very same page, the layout changes, making a relative positioning blank (with background image) space appear in a big chunk at the bottom of the page. Hitting a link to page.php (say a href to the same page as an alternate refresh) gets rid of it, but refreshing just brings it back. Changing the few remaining relatives to absolute makes no difference to the blank space - to the extent where I can remove ALL relative positioning and it's still there. Also do not have any noticeably large minus positioning, like "top:-100px", and such. Yet, it disappears if I simply reclick the link to page.php instead of refreshing. Self taught so god knows what horrifying habits I've picked up, relative positioning being one I am currently phasing out.
The code is very long because it's a very complicated page, half the css taking up 8500 characters on its own (well, I don't have anything to compare to but it certainly seems like a lot to post), so I can't really post it, and I'm using localhost so can't link it either. If it's necessary and some insane person would actually want to read through it, then I'll see about posting it. But generally was just weakly hoping that someone could offer advice simply from the description.
If you are using PHP then maybe through the code you can detect what browser is currently being used and then make changes in the CSS positioning accordingly. For instance, you can detect if Google Chrome is being used and then reposition that particular offending element. Sometimes really bizarre things begin to happen when you are creating layouts in CSS :-). Of course this is not a proper solution. May be something happens with the sessions of the browser.