Check the following KB article to be sure the user you've defined in the Scan Credentials has the ability to run the commands specified:
Once you confirm that, and if you're still having issues, then enable shell module debug:
1) Run Regedit
2) Navigate to:
3) Create the following DWORD value
DWORD value 'ff'
4) Re-run the scan
Check the daily log for any errors... if you can't solve it, open a Service Request and attach the daily log.
Be sure to turn off the tweak after you're done. You can rename it to "__LogShell", that way it's there if you need it again.
I hope that helps!