I was able to replicate the problem. The ship doesn't
launch or dock properly. In both cases it starts to grind against
dock's walls, falls out of sync with station's rotation and is
eventually destroyed.
Good news is that the problem isn't caused by your version of
frontier or your save, Grimble - I was able to replicate the issue using one
of my own saves under GLFrontier as well.
Bad news is that the designers of Anaconda were bunch of morons.
The ship is simply too wide to dock/launch properly with/from
standard orbital docks.
There are three solutions to this problem:
1. Ditch this bucket of bolts and buy a real ship, either some nice
freighter like Boa or Panther, or some good fighter/multitask craft
like Asp, Cobra Mk. III or Viper DC. Remember that bottom turret is
broken in Boa in FE2, though.
2. Avoid orbital stations like plague.
3. Buy a lot of shieldgens and use stardreamer when launching/docking
to prevent hull/equipment/cargo damage.