I have had MBAM Pro for some considerable time and avast and no such issues.
This XP Pro system has no windows Defender and my Win7 netbook has had windows defender disabled since day one.
The difference in Win8+ windows defender is a full blown AV, now when you install a 3rd party antivirus, windows is meant to disable windows defender.
So the problem area is win8 and windows defender, MBAM Pro shouldn't be an issue.
If MBAM though it was a threat it should have alerted, did it ?