John -- Disabling the the shadow copies for your volumes will not affect any other applicatiions interaction with VSS. The VSS services are invoked as needed. The worst part of the scenario is that it destroys the previously made Windows restore points. BESR restore points will still be intact.
Which segways to resetting the security settings. Disable the shadow copies (System Protection) for the volumes, reboot the system, and then re-enable the shadow copies on the volumes. This will reset the security settings needed by System Restore and System Protection, albeit at the cost of losing the previous Windows restore points. Again, BESR restore points will still be intact.
Cheers,
Marco