Code Behind files behave different in both project types. One thing to check is the @Page directive of your pages. To see the differences, and see if you have the right ones, create a new Web Site Project and a new Web Application Project and compare the differences for each Default.aspx and the code behind files. Then check your site and see if you have any differences.
Additionally, check out this page:
http://webproject.scottgu.com/CSharp...Migration.aspx
It shows you how to migrate from 1.1 to 2.0, but I think most, if not all, still applies to 3.5
Cheers,
Imar