Generally if I want to open a mesh in gmax I open it and save to 3ds and it will normally open okay.
There are times I have been asked to make objects IL-2 compatible and usually I ask for them to be sent to me as obj, however, I do not know why but sometimes one obj file will have the parts all over the place when opened and another all together as a complete object.
Another thing to be aware of is that parts such as rudder, aileron and other moving parts are centered in gmax and orientated a certain way so if you take a part from the game and save them as 3ds then open them in gmax that is usually where they will be rather than where you see them in game because your hier places them in the correct place on the aircraft.
Now I have never tried to actually open a complete aircraft, which is what I think you are describing, however, I would assume the parts that are out of place might have been extracted that way and later moved into position in the game with the hier so could still retain their original coordinates from where they were when extracted.
You would need to provide more information I think, complete aircraft? Single meshes?
Please explain exactly what you did.
Anyway, somethings to think about, maybe others can step in and advise.
Hope that helps.
Wishing you all the very best, Pete.