I have had this problem before I just do not remember what file it was I needed to re-upload.
Anytime I update the site, it doesn't want to display the updates(widgets in sidebar, custom header, etc) on the homepage but it displays it on all other pages.
The fix I found before was to re-upload a file from the WP 3.0 install found in the includes folder. My problem is that I do not remember which file it was. Does anyone know which file it is that I have to re-install/overwrite?