I ran into an similar issue trying to book AA and Qatar on the same itinerary. I called in and after an hour on hold while they investigated was told it was an issue with having AA segments on the same itinerary as Qatar segments. I had to book them as separate reservations. I booked the AA segments on one award booking and the QR on another and everything went through and promptly ticketed by the next morning. Of course they don’t know for sure if they will able to check all the way through because of this and may have to enter Qatar to recheck on the QR itinerary but it was the only way to get it to ticket. Someone has clearly screwed the pooch in something.