uh, I'm just reading this now, so I'll put in my two cents. ALL bones must have export transform checked, else wierd things happen. (like what you're describing.)
euh, checking "export transform bone" is so fundamental that it is often considered to be common knowledge.
How the hell do you expect it to behave as a "bone" if you don't tell it to?
Mesh models should have Geometry only checked.
Bones should have transform bone checked.
Mesh parts that also act as bones (turrets, propellors, etc) need both checked.
