Your suggestion might help in some cases, but is not the root of the problem.
I had exactly the same problems when deleting registry entries through reg finder (an the registry entires were not protected or reinstalled). JV 2006 worked a lot faster and finished its jobs whereas JV 2007 was so slow that I could deleted entries faster by hand. (with JV2006 I had to restart the program allover gain after each deletion process however).
I have to go back and use the 2006 version until this is sorted out.
When observing these very slow processes I wished The program had a "STOP" function , to stop the registry search and to be able to apply the changes to the already sorted out keys. Abort - is not as helpful, as onehad to start allover again.