@ zalophus
Whilst this may not be directly related to this possible false positive issue - It isn’t recommended that you have two resident AVs installed at the same time there is a likelihood of conflict at low level driver level.

There is however, a possibility that conflict could have an impact on the full scan, certainly there would be higher resource use (duplication of scanning) and possibly conflict resulting in a BSOD.

So I would suggest uninstalling MSE and see how your system runs, I would say noticibly faster and the same would hopefully true of the Full System Scan.