crabcakes99 I am facing the same problem and despite I disable firewall, anti-virus (Kaspersky 2014) and disable everything that could prevent JV16 to proceed the scan it doesn't works. The same as you, I get the green bar up to 80% and then the process remain as such forever. As you I had no problem at all when using JV16 2012. I reported the issue but the reply I received doesn't very much helped:
"Hello, The Registry Cleaner can show up as frozen if the software does not have the admin access and the operating system is trying to stop the search. Also Antivirus software's active scan can do this. Usually the slowness is caused by other software trying to stop our software from working correctly. I recommend trying to run the software in Computer's safe mode."
If I cannot get it working, I am considering to move back to 2012, which would be very sorry!
Wishing somebody can pay a bit more time to investigate our problem.