I had a problem which was niggling for a while in that I couldn't seem to get Visual Studio (2008) to work properly with Visual Source Safe on my new Windows 7 PC. VSS seemed to work fine when I ran it to view files, etc. For existing projects which I had copied to the new PC, source control integration was working fine.
I then created a new project and needed to check it into SourceSafe. I couldn't get any databases to appear in the "Open SourceSafe Database" dialogue box. It always wanted to default to the local database, which was empty anyway. Even though I could browse and choose the database I wanted, nothing would appear in the dialogue box. After much tinkering and Googling and reinstalling, I finally discovered what the problem was.
The list of available databases is held in registry and even though I had tried manually altering things in there, it seems Visual Studio must have looked in a different location to where I was altering. A post on the internet led me to think of running Visual Studio as Administrator. As soon as I did this, I was able to get the databases to appear in the "Open SourceSafe Database" dialogue box. I then quit out and went back in and the databases now appear correctly.