Version 2.12.660 won't remove the XP SP3 uninstall files, or those for several post-SP3 hotfixes or those for .NET Framework 1.1, .NET 1.1 hotfixes KB25168, KB28366, .NET 2.0 SP2, .NET 3.0 SP2 and .NET 3.5 SP1.
I don't know what the others are it won't remove because I deleted the $ntuninstall folders, which got rid of SP3 and the patches for Media Player 11 and IE7. CCleaner's Registry cleanup then removed the orphaned entries for all those.
So now all there is are the .NET uninstall files. I get no error messages when clicking the Change/Remove buttons in Add or Remove programs.