While your program directories were on the drive replaced all registry entries are still found on the OS drive. That includes installlation logs and folders under your user name in the DocumentsandSettings folder. For Vista that would under the users main directory there.
The registry keys are still there trying to run the games/programs installed to the old secondary drive and need to be removed since the uninstall option probably won't work. Manual edits of the registry have to be done with caution. That's one main drawback when installing programs to other drives.