I booked SEA-SFO-LAX all on CO flight numbers on continental.com, on UA metal. (I wanted to be able to do a 24-hour same day confirmed change with CO's superior rules.)
I supplied my UA Mileage Plus Number, only, to continental.com.
When I looked at the reservation on united.com it showed that my frequent-flyer numbers were:
CO: (CO#)
UA: (UA#)
I didn't think much of it.
Now that I've checked in, I see that my boarding passes have a giant "STAR G" on them and the only frequent flyer number listed is my CO one.
That would explain why my upgrades didn't clear (and now the F cabins are full).
Lesson learned -- always call UA on codeshares to double-check FF#.
Hilariously, even after I change my FF# to the United number, cancel check-in, and check-in again, the boarding pass that united.com prints just says "CO*G" and lists my CO#.
Why I thought I would be on the upgrade list as a 1K: "My Reservations" shows my UA MP number (which I entered on continental.com as my only FF# associated with this reservation) on top of my CO OP number.
Notice that there's no place to edit the FF# here because it's a CO ticket. Here's what my traveler info looks like on continental.com for this reservation - my CO FF# is attached nowhere and never was.
So imagine my confusion when I OLCI to see "STAR G" and "CO*G" and my CO number only, on my boarding pass.
What happens after a little extra prodding: I can get united.com to claim that my FF# is my UA MP#. But even then, Easy Check In spits out this awesome view showing, on a single printed page, two different frequent flyer numbers and statuses for two different segments:
Edit: just for fun, I called both UA and CO.
UA: "I see both your United and your Continental numbers here. We can't change anything about this reservation."
CO: "I see only your United number. No idea why United sees your OnePass number."
united.com support: "I see that both numbers are on there. Would you like me to fix it? OK, fixed."
I love Web support. Don't ever change, guys.