I'll never forget a needlepoint carefully hung on the wall of a friend. It read, "Our Home: Clean enough to be healthy but dirty enough to be happy."
Juice contributor fbuonvino points out that the same philosophy should hold true when using registry cleaning tools to tidy up a machine that's housing virtualized applications.
Special care should be taken during registry cleaning on a machine using SVS. A program like Registry Booster or similar, normally used to clean a registry of errors, wrong paths, and open links could possibly mistake registry entries belonging to virtual applications as problems to be dealt with -- if the application is not currently activated.
You could easily verify the problem by making two scans, one with your virtual applications activated and another with those same applications not activated.
I've found that if you scan a registry without first activating the virtual applications, and then continue with the error correction steps, you will damage the virtual programs.
My Test Cases
As an example, having on my PC about 40 programs in my SVS list and 60 outside SVS. I scanned and found 1045 errors with all my virtual applications deactivated.
Doing the same scan with 20 programs on my SVS list activated, I found only 724 errors.
Finally, with all the programs on the SVS list activated, I found only 325 errors and after correction I did not find any problems using the virtulized programs.
Increased Scan Time
A straight consequence of making a scan with all virtual programs activated (active, not running) is that the time necessary for scanning is much longer as many PC resources are used.