Similar problem
I had an itinerary booked through AA.com as American, operated by United Airways. I flew from AUS to PHX then PHX to YEG.
The miles and segments never got credited to me. I flew back from YEG to DFW to SAT on a different ticket, AA metal.
American claims the ticket was "still open" and that I hadn't taken the flights to Edmonton. After some complaining, the phone agent was going to check with US Airways and get it sorted out... but about a week later, still no miles. So, I have another complaint in to them about not getting a response or help.
Lesson learned - avoid flying US Airways metal until they get this all sorted out?