On thing that I have done in the past is grab the source code from your home page, and also from a working page (use View Source).
Now paste that source into a diff tool such as Diff Now
Often times when I do this I find some dumb mistake that I made (as others have said, it looks like a div not being closed or is nested on accident). The technique has saved me hours in the past.
Also, look into something like "clear:both" or a "clear fix". Might be the issue as well.