Well duh.
Blender will NOT fuxor anything up, IF it's done right. If you mess around like a proverbial hippo you'll end up with crossing polys, extra verts, non-flat polys and crap like that. Those are what **** up conversions.
You DON'T do subobjects in Blender. The hierarchy for .dxf models is totally different from .cob, and you WILL end up with a fuxored up ship.
Besides, Maya owns both LW and MAX, but damn it costs a hefty load. Lightwave owns MAX, in modeling, animation and rendering, as soon as you learn to use it properly. And no ghey icons either.