I've had similar issues happen before.

1. Get a United Service Director (not front-line agent) on the line, ask him to pull up your United PNR, and compare it to the PNR on the Continental side using the CO record locator -- the SD will see any discrepancies going on, and place you on hold while getting either the Support Desk or a CO agent on the phone to ensure the right flights are showing up.

2. The SD can also place you onto another UA operated PIT-ORD flight, and confirm your upgrade on the spot, free of charge if you explain what happened and politely but firmly request to remain on United.

3. Select seats for UA flights through UA, and for CO flights through CO. It's the easiest way to get the seats you want.

Problems solved. Let us know it goes.