This doesn't directly answer your question, because as Cheryl says, it is difficult to troubleshoot an issue such as this without seeing the page and code and, preferably, the CSS. The issue of positioning is quite complex, due to the both the fluid nature of the medium and to the differing implementations across browsers and CSS versions, and has spawned books, Web sites (check out "Position Is Everything"), and innumerable tutorials, so your question would not admit of an easy "here's how you fix it" answer in any event.
However, there is a tool that I have found to be extremely valuable in tracking down issues such as this, called WebTools Pro. I should say up front that I have no connection whatsoever with Iconico, who produces this software, other than satisfied customer since I purchased it in 2004. Anyway, this software has a feature called Page X-ray which allows you to put colored borders around various page elements--divs, images, spans, etc. You just click the desired element in WTP to enable or disable the color highlighting. This works on the page AS RENDERED, after any DOM manipulation, etc. It helps finding unexpected nesting, broken nesting, etc., and I've found it invaluable in troubleshooting complex page layouts.
I do this stuff for money, so the cost ($19.95 in 2004, $29.95 now) was negligible compared to the productivity increase gained. Hell, to my mind, for anybody who plans to do a good deal of Web design/development, it's worth it. The good thing is that they have a trial version that you can use, and if you decide it's worth the money you can then invest in it. There are many more features than just the Page X-ray, but since that touches on your problem I thought I would mention it. Check it out here: http://iconico.com/webtool/
Try it out and see if the Page X-ray (or one of the many other tools) helps you locate your issue. It's up to you whether you decide to go with the full version once the trial expires, and you lose nothing either way.
cheers,
scott