Oh, it seems to be docking-related.
I could attach the mission if you want, but here's some relevant information:
I have a
AK FR Cintamani warping in via hyperspace (star wars) style warping with the following setup:
Tail <- Docks <- Head
the Docks module has three transports docked to it in addition to the head (The tail is the one with the 'arrival cue')
Shortly after arrival, the three transports are jettisoned and given orders to fly waypoints.
The crash itself occurs either when the train warps in (during a cutscene ~30 seconds into the mission), or later during the mission after the train and the transports have been ship-vanished at the end of the cutscene.
EDIT:
if anyone on SCP wants to actually play through the mission with the modpack and all to pinpoint the error, could give SVN access.
if the mission file is all you want I can just post it.