Well, I have Revo Uninstaller, and when you uninstall a program it searches for left over files and registry entries. So I guess I'll download and reinstall versions .11 and .12, then uninstall them with Revo to make sure everything's gone. Hopefully that helps fix the issues.
Edit: Does anyone know where I can download older versions?
You say you deleted .LMMSRC but have you searched for files with a wildcard at the end to try and get more hits? Ex. If you search for lmms* in unix/linux you would find all packages that begin with lmms.