I am a little closer to figuring out something... When the seat map for the bus "flight" shows up with only 2 seats, the computer doesn't know what to do with that segment. When the seat map shows up properly with 24 seats, then I'm able to checkin because it knows there's a "flight" there. Airport agents have said that sometimes the bus flights read as "open" segments with no equipment/vehicle and so if you can't get a seat (since there are no open "seats" to begin with), then you can't check in. I've tried to contact IT and such but with no avail. Many people on the ABE/EWR bus I've talked to said they have this same problem...