I've run into this problem with United flights before. My recollection is that Citi PremierPass started being able to automatically process United's domestic destinations where United was putting in city codes instead of airport codes (e.g., CHI, NYC, WAS), but as recently as this year, I was still having problems with points posting for flights to/from London (LON instead of LHR). They might have gotten enough complaints about it to add the city codes to their database, for example.

However, I never had to actually FAX in boarding passes -- I would talk to a manager and have them look at the flight information passed from the airline to Citi, and they'd make the necessary adjustments that would post with either the next statement or the one following that.