I had something similar happen to me on a *A partner booking. I had used AC miles for a roundtrip ticket from LAX-JFK on UA over Thanksgiving. Originally I had booked in C, but then I had to change my times and only F seats were available. I had no problem on the outbound leg, but when trying to get on an earlier UA flight to LAX when checking in at JFK, the ticket agent informed me that I didn't have a F ticket according to my reservation and Air Canada had only booked me in business class, which was crazy because I had been on UA's website that day to check my seat assignment and they had me booked in F. I thought not a big deal and was ready to take the seat and fight for the miles back when I returned, but there were no available seats in C for the rest of the day. I brought up the reservation on my phone which had ticket numbers and everything, and he still wouldn't budge. I even tried calling Air Canada, but they couldn't see how UA would show it as a C ticket and he refused to speak to them (I was stuck as the middle man). Finally, I don't know if it was persistence or frustration, but after about 30 minutes of trying to convince him that I indeed had a seat on the plane (as I said, I was perfectly fine going back to C if they had had any seats to give me) he threw his hands up and handed me a F boarding pass for the earlier flight. I asked if he had figured it out, and he said no and didn't really explain further.
Basically after that, I learned to be judicious in changing my award itineraries for partner bookings (I had never had problems before even with my award booking last summer using NH miles on an itinerary that combined NZ, OS, and LH) and also VERY CAREFUL in making sure that I had all of the confirmation numbers and actual ticket numbers and to check the classes listed with each airline to make sure the codes match up (apparently the AC code for first is the UA code for business or something). Usually there is nothing to worry about when making a partner booking, but until they are all matched up on the same computing system and use identical codes, its important to pay attention and make sure nothing goes wrong.