Try this. It will run the scan silently. It still takes just as long but you can check it later.
c:\Spybotinstalationdirectory\sdscan.exe" /scan /silent /taskbarhide /autoclose
Then just open the system scan, stop it and check the recent scans. It should be in there. Or you can navigate to
c:\Programdata\Spybot\logs\
And find the file name "Scan Results.YYMMDD-HHMM.txt". You can review the results here and try to clean them up from within the system or if you want to clean them all just run
"c:\Program Files\SpybotSD\sdcleaner" /silent /taskbarhide /autoclean /autoclose
This will clean silently as well. It does not fix the problem entirely, but I do not notice much impact when I run it this way.