I tried the same experiment as before:
(1) Cleaned the registry (using 2nd most aggressive scan) and fixed/cleaned all errors.
(2) Flushed/Rebuilt JV16 PowerTools cache and scanned again, finding 242 errors. Fixed/cleaned them.
(3) Reinstalled JV16 PowerTools and scanned again, finding 4 errors. These were from temp files so they may have been made in between uninstalling/installing JV16 PowerTools.
I would like to see some other users try the same experiment and post the results. Based on these two tests so far I would say to get the best results from JV16 PowerTools to periodically flush the cache and perhaps and occasional reinstall.