Sorry if this is a dumb question. I flew today from DUS-ORD-DEN and when I made the booking, called AA to apply a SWU. I also requested the domestic upgrade from ORD-DEN using the online check the box feature. I was waitlisted for both.

I didnt clear the DUS-ORD sector (no big deal) and obviously when I checked in at DUS this morning German time the agent printed both boarding passes.

When I get to ORD today, I check my reservation on my iPhone and noticed the upgrade list (and I was no where to be seen)

The nice AAngel at the Flagship lounge checked, tapped furiously away and then said refresh your screen, and voila, I pop to number 1.

Am I doing something wrong? Should have I checked in online? I have no clue as to how the domestic upgrade process works. I'd like to understand if these are one off glitches or its just the way it is...