I fixed this some time ago. I eventually did go back to using a table for the layout (which I understand is frowned upon) combined with a little bit of relative positioning, but I made sure everything was done with css and was w3 compliant:
The inherent problem, I think, is the way I designed my older pages, visually. They were highly graphical and usually made up of one contiguous background image, with a lot of art making up the section borders, etc. The general layouts tended to be unusual shapes, and I would then over-lay text and content on top on that. Unfortunately, it's very difficult to get looking right if the sections are separated.
I've since designed newer pages using only divs and css and it seems to work well, although it's a bit trickier to get working. The key, I think, is to come up with a look and style that I know is going to work using that technique from the start.