I am not sure what you mean by "stall".
If RegVac has a problem, it (not Vista) will give you an error. If it does not give an error, then it is still working and you should let it continue working. That part of the registry does take a while to scan.
My guess as to what you mean by "stall" is that Vista has told you that RegVac has stopped responding. This is something Vista does but it does not mean that anything is wrong. Vista periodically sends a message to programs that are running and the programs are supposed to answer back. When a program does not answer back within a certain amount of time, Vista assumes that it is not running and so Vista gives an error saying that the program has stopped responding (XP did the checking too but it did not give an error as Vista does).
If the program is too busy working, it will not respond in time and you will get that error.
So if you are getting that error message, please let RegVac continue to work. Do not shut it down and you will find that it will complete the scan. This is more a problem with Vista and not RegVac.