an update from me as well.....
i rec'd the same error for my sfo-jfk-sfo m/r this weekend and could not check-in on line or with mr/ms easy at sfo. however, it turns out that my issue was that my m/r was a re-book due to a weather cancellation (blizzard) back in january so it looks like that if the tix is re-booked (even though the original purchase was done on-line), you won't be able to check-in on-line.