Get the newest version of PCS, the bounding box problem was a bug that Kazan has since fixed.
Crashing issue...
Polys that aren't flat (all vertices must be coplanar)
Too many polys in a single subobject
Polys that don't have a texture applied
Textures that aren't the right format
Quickest way to see if a POF is going to immediately crash FS2 or Fred2. Rename your POF fighter01.pof (the Uly). Go into the tech room and see if it displays.
Isolation methods: Save the COB under a different name. Edit the COB and take out everything but the base model. Convert it to a POF and see if she works. If so, add the next section (next LOD, debris, etc.). Continue until you find the one with the problem. If the main LOD crashes it and you have textures applied to all surfaces and you are sure the textures are 256 color PCX files, triangulate the model and retry. If it works then, you have a problem with a face or faces that aren't flat.