I don't know if old one did registry entries but it did check just the files that are used in the CRC calculations.Does it check any files that are outside the program install path that might not get removed by an uninstall? Also does it look at specific registry entries that I might have missed when I searched the registry?
BTW, did I ask you if you were using an account with admin rights? I hear that there is something going on with CRCs when not using admin rights.