It almost sounds like when the policy completes it's not reporting back to Jamf that the policy completed. I get that sometimes where the computer doesn't report back right away and the log will say that it wasn't reported at the time of completion. Any way you could perform "jamf recon" at the end of the policy? I generally just leave it and eventually the computer will check in again and report back to Jamf, but "jamf recon" should theoretically speed up the process.
The other option, if that doesn't solve it, would to create a smart group to scope out the computers that obviously have it completed and exclude the smart group from the policy. It may not show that those computers completed it in the logs, but the smart group would remove them from having the policy applied over.
Hope this helps.
