I would appreciate some help with a recent missing Avios/TP claim which I believe was incorrectly rejected. No reason has been provided yet but I am pre-empting possible explanations for the rejection.

Background
I bought a QR-issued 157-ticket (BER-DOH-KUL/BKK-DOH-MUC) for travelling in Business Class (in "I" fare class). Three of the segments (BER-DOH, BKK-DOH, DOH-MUC) were operated by QR and the appropriate Avios and TP have been posted without issue.

The problematic segment is the DOH-KUL sector with QR4991, which is a codeshare flight operated by Malaysia Airlines. This is also in Business Class ("I" fare class). For the avoidance of doubt, my ticket has the QR4991 flight number, rather than MH161.

Flight
When I checked in at Berlin, QR was not able to issue a boarding pass for the DOH-KUL segment even if they were able to check in my luggage all the way to KUL. Neither the transit desk in DOH nor the Al-Mourjan lounge was able to issue me with a boarding pass either for DOH-KUL as apparently "I was not checked-in". I was only finally issued a boarding pass to KUL at the boarding gate - literally, as everyone else is boarding. My luggage arrived in KUL without any issues.

Fare class
I am aware that I class in MH does not accrue any Avios or TP. However, as mentioned before, my booking has the QR4991 flight reference. So, I would have thought the Avios/TP should be based on the I class for QR, not MH.

Am I correct in that this should be an Avios and Tier Point earning fare in BAEC? What would be other possible reasons for the rejection or how should I approach this?

In any event, BAEC was not able to provide me with an explanation either and has re-submitted my claim.