I agree there is not a seamless integration between the UA and CO systems yet

I had similar difficulties on my SFO-EWR yesterday. Granted it was platinum heavy flight and did not get my hopes up. However, I would have liked to have at least been listed on the upgrade waitlist. After check in and still not on the list, I asked a PC agent to look at it. He finally got me on the list but my wife never did show up. I was told that since my first flight of the day had been EUG-SFO on UA and the SFO-EWR was on CO it messed up our status. Makes me wonder if we had been on at the 5 day mark would the mileage upgrade had cleared? Maybe. I guess I'll never know.