I flew into and out of El Paso from Phoenix last week and I was not auto upgraded at the window either but did sit in F on both flights.

PHX - ELP Mesa Operated (US Marketed) Upgrade offered at online check-in

ELP - PHX Mesa Operated (AA Marketed) Upgrade not offered at online check-in so I asked the AA desk agent in ELP and she processed it for me and was surprised I wasn't charged a fee, even though I am CP.

On another note, I overheard the MESA flight attendants complaining that they sometimes fly in as a US Airways marketed flight and turn out as an American Airlines marketed flight and that there are differences in service and announcements even though fell they should be the same.