is this issue occuring on Single player or multiplayer or both? if on SP try typing the command "/force_save" and then exit the game.
also when you go into the nav menu (N) you dont find your ship in the list of near objects? or the find last ship button, cannot find your ship?
also when you sign into the game, you will always be in astronaut mode. so if you sign out while in a ship, you can expect to sign back in, in astronaut mode, and just out side the ships core. but in this case you say your ship is completely gone, so that is indeed a problem. (movement while signing out shouldn't be a problem as after a test of signing out at fullspeed, i signed back in right next to my ship core, so the game seems to kill your ships velocity when signing out, which is overall a good thing)
let me know if the force save command works or not. if not, then yes, plz provide a log and ill send it to the test team. the logs can be found in the logs folder of your SM installation folder. the log with the number 0 should always be your most recent log, and then 1 you second most recent 2 your third most recent, and so on.