Are there any errors reported in the conversion report? In mine there was an error with the page that had the calls to System.DirectoryServices. It also seems to me that building web projects in VS2005 is buggy. I seemed to get different errors when I tried to rebuild, without changing anything, or if I had a different page open.
If I remember correctly, most of my edits dealt with either modifying or deleting the "inherits" attribute from the first line of the file.
I. Kinal