From my past experiences, you need to check-in on CO separately after checking into UA to get on the upgrade list -- they don't play nicely and probably won't until the merger. If I fly UA then CO, I've done this by just arriving at the airport and asking for my boarding pass at the CO desk after checking in my luggage at the UA desk (this isn't always possible -- I know).

As for the other incident about you being canceled, I think (just a guess) your reservation might have been rebooked after your flight (possibly) reported delays longer than 10 minutes and the UA system took over thinking you were going to miss the flight. I've had incidents where there was trouble at the gates and had the UA system rebook me with me arriving only 10-20 minutes late with having plenty of time for my connection. However, the UA system would've booked me on a later flight with a weird routing. I usually take it and hope for Y credits though .

I'm not sure why your reservation would be canceled -- that remains a complete mystery to me.