I had the same problem with an IAH-SAN. Waitlisted using a GPU.
The DCA-IAH was available when the GPU was applied.
But the IAH-SAN - open R1 and my waitlist did not clear.
On UA.com - the waitlist for the segment no longer showed waitlist like it had, but the upgrade had not cleared.
I called UA and got a supervisor (out of Chicago - a legacy UA agent). After about 1/2 hour - she worked and cleared.
I told her the waitlist no longer showed on UA.com but I hadn't cleared. I asked to speak to tech support (legacy CO tech support) but she couldn't get through. In the end she cleared it - and then of course R went from R1 to R0.
Had someone called in when R1 was showing they could have grapped the upgrade over my waitlist.
All this is really not satisfactory. I know there are glitches and eventually this will be resolved. BUT the best thing UA can do now for customer Satisfaction is SHUT DOWN TOD's.
Until UA does - I am flying AA.