Been spending spare time playing around in Apollo and I found the boarding priorities for each of the UAX carriers. Each different carrier has their own priority scheme.
I'm not positive about this (I've never worked in CS for a UA/UAX carrier), but I believe the priority sorting has to be done manually by the agent. Therefore, it is possible they may be sorting them incorrectly. They can look at
S*UAL/UAX-OMC in Apollo to view proper priority for each UAX carrier and the procedures to follow. That said, I wouldn't go accusing a gate agent that they don't know how to do their job...that's a quick way to the bottom of any list.
If I read correctly, pilot772 is almost right. At the moment, there is essentially, there are 2 sets of UAX OMC priorities. AX, G7, RP/S5 go by company pilot/dispatcher, UA pilot by time of check-in, UAX pilot by time of check-in, all other OA by time of check-in.
It would appear that OO and YV mix in the UAL/UAX Pilots together by time of check-in...
SkyWest is as follows:
-SKYWEST PILOT BY SENIORITY
-SKYWEST DISPATCHER BY SENIORITY
-ASA PILOT BY SENIORITY
-UAL/UAX PARTNERS BY TIME OF CHECK-IN
-ALL OTHER
Also, on OO...ASA Dispatchers fall in behind OAL pilots and before other airline DXers (if we had our way, ASA DXers would fall in before OAL pilots

).
Hope this helps, feel free to PM me with questions.