Seems like there are several easy solutions to this but with commuting getting so difficult lately people will do ANYTHING to get a seat. If a UAL pilot saw a UAX pilot (don't tell me they can't tell) they should have also said to the gate agent that he may not be of the highest priority.
This goes back to a general lack of respect SOME mainline guys have towards regional pilots. I have actually been told by an AA FO that he gets the jumpseat over me on a NORTHWEST flight even though I was there about a half-hour before him because "You're Eagle, I'm AA, its my seat." to which the NW responded by clarifying that its first come, first serve with off line and non-Airlink pilots, and that this AA guy should find a different ride to work.
Its a slippery slope UAX and UAL are on right now, hope it doesn't all crash at the bottom.