Had the same problem last night with the ship of my soc. I wrote down the coords after landing there and later went back to those coords. There was a ship in the bay (as i expected) but i couldn't enter the ship. Tried refueling it to see if it was "mine", but got the message that i wasn't the owner and couldn't access it.
Checked coords again and again, searched the other bays, relogged and tried again, but all to no avail.
It was only then that i realised it might be on the other level. There is no signpost or whatever there to tell you on which level you are and oddly enough i never really let it sink in there actually ARE 2 levels, until i studied the map a bit more closely and noticed the overlaying bay images. All the times i was up there before, i probably just had the luck to be on the right level straight away. Although that hasn't been more than a handful of occassions since it's not my own ship but the soc's.
So, Neomaven is right a couple of posts back. Your ship is more than likely on the other level, and navigating to get there is a true nightmare. There's no indication on which level you are whatsoever, apart from the 3rd coord in the display (which i didn't wrote down when i landed). 1st level has an altitude of ~100, the second level of ~120. As far as i know, that's the only way you can tell them apart.
Very frustrating if you can't get to your ship in a reasonable amount of time. MA really needs to add some better signs there.
So, go to the bay you think is the right one, check the altitude if it isn't your ship, and then fiddle around till boredome strikes to get to the other level.
My bet is your ship will be there then, worked for me
I wish you a lot of euhh... *cough*.. fun