This happened to me for a while with OZ (Asiana). Showing the card took care of things, though it also almost always required the intervention of a supervisor to waive whatever fees the UA system was trying to charge me for bags. Showing the card at the gate together with the boarding pass was enough to get into the early boarding groups. Funny enough lounge access was never a problem (that system had the correct status info). And CO always had the right info in both their res system and their lounge system (if I recall correctly, this was before the systems merger on 3/3/12) as did US, LH, etc. Just UA didn't. After 3/3 everything was OK (probably the only good thing about switching to SHARES).

Anyway, the take away was to always carry the card and, if necessary (and again, this was VERY rare), to gently but firmly insist that the fact that UA's system was out of whack with reality and the rest of the world (CO, UA, LH) was not my problem and that I expected to be accorded the benefits I was entitled to while sympathizing with the agents that it was challenging for them to override their system.