Start script wil not stop after deleting

We had a virus hit our network a few weeks ago. We tried running Microsoft’s MRT tool and it helped to a point. After we cleaned every computer, we created a group policy as a logon script to run the MRT tool. We thought this was a good idea, but then users started complaining that it was taking any where from 5 to 10 minutes to login in the mornings. We unlinked the policy from all OUs, but some computers are still running the script. We unlinked the policy about a week ago, so there has been enough time for the policy to update on all the computers. Anyone have any ideas?