Join Date: May 2010
Location: PHL
Programs: AA EXP, UA *S, Hilton Diamond, Marriott Titanium, Hyatt Exp, IHG Plat, National EE, Sixt Plat
Posts: 648
UA's system for a while was sending over the booking class flown rather than the booking class purchased, which was causing a zero-credit problem in this scenario when the miles actually went to post. A call (or sometimes a few) to US could get this resolved, as bevoinva said, with a little persistence.
I don't know if that's still the case, or if UA now sends over the correct information. It's been a while since I've seen this topic come up, so maybe they have fixed it. Or maybe everyone is just avoiding UA like the plague, or still sitting at #89 on the upgrade list for an upgrade they're technically not eligible for anyway (unless like in OP's case they share a PNR with a UA elite).