Hi,
I use CCleaner as well and have had the same thing happen. I have a good sized list of several obsolete registry entries in CCleaner which I have been unable to pick up with JV16 Power Tools 2009 or 2010. Now, overall, I have found far more entries with JV16 Power Tools to clean out than with CCleaner, and it also emphasizes safety. So I think JV16 Power Tools is certainly better. I do know that several of these entries (if not all of them) can be safely deleted (on my system anyways). For example, I had the trial version of ZoneAlarm installed about a year ago but decided to use Norton Internet Security instead. After uninstalling ZoneAlarm, JV16 Power Tools was able to find and delete several entries left behind with both the Registry Cleaner and the Software Uninstaller. But there has been a single entry that CCleaner is able to pick up that JV16 Power Tools has not been able to. I have not deleted these with CCleaner yet because I was trying to use JV16 Power Tools almost exclusively, but have yet to get JV16 Power Tools to find these entries.
*EDIT* - I have attached pictures of CCleaner to see the entire list of registry entries it finds which JV16 Power Tools has not been able to find.
CCleaner - Registry List (1).png
CCleaner - Registry List (2).png
CCleaner - Registry List (3).png
CCleaner - Registry List (4).png