eh? .. how did they get infected?

sandboxes are complicated, and if not setup correctly they will be next to useless. Sandbox are very safe if you know how to use it properly.

I use a more simpler "sandbox" called returnil. This put's your entire c: drive in a sandbox. While you are on the internet anything you download lives only in the sandbox. When you reboot everything that occur while returnil was enabled is deleted. No virus/spyware has ever survived the reboot.

Another free program that just came out "comodo time machine" can be consider a "sandbox" program. It makes a baseline snapshot, which you can always go back to. You can install programs/utilitys to test etc on a different snapshot, if you get spyware/virus just restore a previous clean snapshot. That's probably the type of program you need so you can "test" your utilitys on a snapshot without damaging your windows.