When you say he’s looked at both do you mean he’s looked at the RAW CDR before it hits the MDR-2000?
If so, then your back to the PBX reporting this data as is. In other words what shouldn’t be happening is happening.
If not, then you need to, the MDR-2000 as you may already know takes RAW CDR and chops it into small little chunks, discarding what it’s not instructed to get as well as null spaces. Thus it’s able to store more records in a smaller amount of memory. Again this may be repetitious, but hey I’m bored!
From a troubleshooting standpoint I’d focus on comparing RAW CDR (Not from the MDR-2000) with the MAT Data. This way you can quickly narrow down the culprit. I honestly see you doing this faster then finding someone else running a similar configuration without the problem.