Had a very similar problem; despite 2 phone calls to UA 1K line and 1.5 hours on hold (with some very nice people) it was not fixed;
Once I got to the airport it was fixed and I was upgraded right there.
I was upgraded because first was not full.
So from now on, I buy the ticket on the site that I will fly more segments or have the segments that I want upgraded the most.
It is not helping my trek towards the million mile mark unless the new UA mileage plus will add up the CO and UA lifetime miles.