I think I'm seeing the same thing on Windows XP Pro SP3. I ran two other "registry cleaner" programs and they both detected over 400 "Invalid Files and Destination Folders." jv16 PT2009 1.9.0.580 didn't detect any of these.
As posted in another thread, I spot checked a number of these errors and the "C:\ path" for the file or folder indeed does not exist (probably the file or folder was deleted long ago).
"Invalid Files or Folders" http://www.macecraft.com/phpBB3/viewtopic.php?f=21&t=3834
As was suggested in that thread, I did submit a "bug report" but have not received a confirmation it was received, logged, accepted, etc., so I can't give you a status of that report. I don't think the "bug tracker" status had changed since late in May.
I originally thought I had missed an option or setting that was causing the Registry Cleaner to ignore this type of error.
It appears that its probably safe (in my case) to delete all these Registry Keys - but I'd rather they show up in the Registry Cleaner results and let PT "fix/delete" them so they could be backed up first.