This is for jv16 PT 2011, V2.0.0.1007 on Win 7 SP1 x64 Pro and Win 7 SP1 x86 Pro. And I feel confident that it applies to 32/64-bit Vista systems as well.
If User Account Control (UAC) is active, Phase II of registry compact does not run. UAC is silently blocking RegCompactPhase2.exe when the system boots up into Windows following a Phase 1 completion of registry compact. No Phase II command prompt window appears and the registry compact is not completed. No UAC alert window appears asking permission to run RegCompactPhase2.exe either.
If UAC is then turned off and the system rebooted, the Phase II command window appears and the remaining hives are then compacted. Thus RegCompactPhase2.exe has remained queued except an active UAC is preventing it from starting.
If the Compatibility of RegCompactPhase2.exe is manually changed to "Run as Administrator", this change has no affect on the above failure if UAC is active. This bug is 100% repeatable.
Another minor bug is that the Registry Compactor title states "jv16 PowerTools 2010" instead of "jv16 PowerTools 2011".
Submitted to Bug Tracker....which incidentally is not being maintained for users to see which bugs have been submitted/rejected/fixed etc. :?
(And wouldn't ya know it. This bug surfaced as I was expounding the marvels of jv16 PT after installing it on a friend's computer and teaching him how to use it. And his registry had never been cleaned or compacted during 4 years of Vista and now Win 7. : )