So you are saying this was a DL 006 ticket? How did you buy the ticket? Normally a DL-coded X fare on partner metal would earn full miles unless it was a consolidator ticket (in which case, it would only earn 25% MQM/miles).
I lost miles on a similar X on KLM routing during IRROPS last spring- had originally been something like a V class, but got rebooked as a X/M for the AMS-EDI leg, and there were enough things that went wrong with that rebooking, I ended up just standing on the compensatory miles that customer service was throwing at us and not chasing original routing credit because they'd burned me out at that point.
(Yeah, bad FTer there)