This happened to me in the first part of the OP.

When I checked in, both co.com and the pda site showed that I was in seat 1-E. However, my boarding pass showed "CHECK IN WITH GATE AGENT" (original in all caps). When I got to CLE, I showed this to an agent in the PC and she said she had never seen this before. I was indeed not checked in, although I was holding a boarding pass for the flight. She did some kind of override and handed me a BP with my seat assignment and informed me that I was now checked in. This was 40 minutes prior to scheduled departure.