This just happened to me on a Y ticket that I bought inside my upgrade window. I requested complimentary upgrades. Segment 1 cleared immediately, but then I couldn't check in. According to my corporate travel agent, the reason is that the upgrade cleared before the reservation was even ticketed, so there is a discrepancy between the Y ticket and the F seat showing on the reservation. She says there is no way to fix this except at the airport. Frustrating, because the delayed check-in means I will be low on the airport upgrade list for segment 2, which has not cleared and is going to be a tough one.