You set up the subobjects in the LODs wrong. Can't have same-named subsystems across LODs.
Game gets confused or something.
Go armora for detail0, then armorb for detail1 etc.
Same for the turrets that have LODs : turret01a turret01b etc.
Then for the live debris it should be debris-armora01, etc
You also have a lot of random non-subsystem subobjects that should probably just be fused into the main hull.
And it might have too many thrusters. IIRC its 24 max (for ships with afterburners its 12, since 12+12), unless that's been bumped.
Also you probably want to de-parent the Drone Panels from Drone Control. No reason to have a subsystem parented to another subsystem (that's rotating!), that's just asking for trouble.
The collision box doesn't follow it during rotation etc, it just plain doesn't work well.
FSO would probably be okay with most of what I listed, but since it's not how I like to set it up (which definitely works), it's wrong.
