Do you have more than one flight on the reservation? I had that problem a couple of weeks ago and they said it was because I wasn't within 24 hours of the connecting flight. She said I had to wait for T-24 of the local time of the second and last flights before I could check in online for ANY flights on the res, which in my case, was SEA time which was 3 hours different than where I was.

Seemed strange to me as I take the same flights regularly and I have never had any trouble checking in for all downline flights once I hit the 24 hour mark of the first flight. But sure enough, about 9 hours later at T-24 PST from flight #2, it worked. Not sure if this is a new change but if so, it is a real pain as I am often in the air prior to T-24 of subsequent flights due to time zone changes, length of flights/connections etc.