It may be the agent is using an OTA to book the rooms and that could be causing the failure. Or they are not submitting your MR number and giving it to the front desk could help. I also recall reading about a manager booking his staff's stays under his account to get the credit (seemed worked more often than not). Maybe that's "part" of their compensation.

And, actually, it's master bills that would not be covered, but direct bills would be ok.