He was a Windurstian taru no? Not Sandorian? Maybe that Brugaire quest thing where you smuggle goods tripped him up with contraband (or contraband items that he accidentally got from the Goblin box or MG Flotsam?) and he doesn't have access? Or is it he actually just gets kicked off of the airship after he boards properly, by a glitch?
He is windurstian, however, he hasn't undergone any tenshodo quests, nor does he have a regular airship pass, so it's extremely unlikely that is the case. What happens is when he goes on board and the cutscene of the airship takes off, it immediately rezones him back to Port Jeuno instead of being on the airship.
I think he has to do a reinstall, because I logged onto his character on my PC and it let me onboard. Something's messed up on his side somehow; and the POL file check found nothing ;/