Ships don't dock...

[Plunderin Mom]

I haven't had that happen, but I did "lose" my ships once on beta. When I went to launch there was no ship to launch. I remembered somebody else here saying this had happened to them, so I sighed and then spent the hard earned gold I'd been saving for a bigger ship on another midsize frigate, only to have the first one reappear later...

[Thalore]

I've had this happen a few times, mostly when I go to Driftwood for some reason.

There is a much simpler way to fix it than killing yourself though

go to your ship
have someone come to you
log out (completly)
log back in, then have the person leave your ship.

It has worked for me every time this has happened. and yes I have reported it.