From the OP's description it could all be normal (or there could be a problem). AA flights do book into A for US domestic on a D fare (enjoy!), so that part is normal, also normal not to have all flights show up in a single airline's system for various reasons. The acid test is precisely the ticket number, as suggested by christep. You need the ticket numbers in any case -- they should be at the bottom of your confirmation e-mail. This is that long circa-16 digit number that starts with the 3-digit airline code (001 for AA, for example). You need to always have the ticket number with you when you travel using e-tickets; if the airline cannot find your ticket when you check-in, the ticket number must be supplied by you (and then they can usually find it a different way). For e-tickets, this is crucial. And once you have a ticket number, everything else is irrelevant.