as far as i noticed after some tests, the problem is not related in any way to the "quality" of the geometry, it doesn't matter if you use or not booleans, intersecting polys, faces with more than 3 vertices or other odd strategies
it seems instead something related to the shape, sometimes you get better results using cob2fs2 or pcs, but sometimes you have problems anyway, like if fs2 has some problems with "non solid" objects. with "non solid" i intend a shape with a lot of parts that came out from the general body
for example an xwing has the long nose, the wings, the laser cannons, the engines thrusters, the laser cannons, i also have a similar but very very smaller problem with the tf and ta solar panels
the mass setted in pof edit also seemed to have a certain effect in reducing the problem (but may be wrong)
the speed at wich collision occurs also seems to play some roles: sometimes you detect the problem only rotating the model at zero speed, and if you engage top speed sometimes the problem disappear
another thing noticed is that sometimes when this problem happen you can even shoot through the model
the size of the model also seems to don't have effect, its true that i tried only fighters but i also tried models with size 50x obtaining exactly the same result
i already have to try instead to split the mesh in subobjects or to work with eyepoint