I had this exact issue last week on SFO-IAH-FLL. Booked through CO, all CO flight numbers, CO Plat # on res, but the SFO-IAH was on UA metal. There was plenty of upgrade room on SFO-IAH, but my upgrade did not clear in advance (IAH-FLL did). I asked at the RCC the night before and they said that I was never on the list and they do not know why. They manually put me on the upgrade list and I cleared at the gate.

For some reason, these mixed CO/UA metal itineraries are not upgrading properly.