Just for the record.

changing the gunboat encounter to sc_fighters means you will only get fighters unless you add gunboats to the sc_fight class. Basically all you've done is disable gunboats.

You can make gunboats fighter class in the shiparch.ini too. Thats another way of getting gunboats everywhere that fighters would normally appear.

Giskard

damn, sry for picking up this old thread but:

i encountered that problem, docking with a tradelane and then crashing to the desktop.
for me it was somewhere in bretonia.. but it doesnt matter at all because this bug is not system-related...
my error in the mod was the

mission_property = can_use_med_moors

in the shiparch.ini of a transport that i made flyable
i changed it to like

mission_property = can_use_jumps

or something like it and this caused the crash.
even removing the mission_property line completely will cause that sort of crashes (mostly entering a tradelane when an encounter with that transport spawns)
i assume because FL cannot handle the unknown or not available mission_property value