Just to perhaps clarify what you my be able to do to fix it:-
If your SUR file is about right and in one piece (i.e. no breaking-off parts), all you need to do is load the .CMP model file into FL Model Tool, and then save it again immediately without resizing or anything - but don't overwrite your last copy of your .CMP or .SUR files though, just in case!!
What you will see that FL Model Tool does is to recalculate the centres and Bounding Box Radius of the .cmp model as soon as it loads it in, and gives you the option of saving the new centre and radius values.
Then just to be as good as possible, load up your SUR file too, resize it to the .CMP file, making all components part of the hull as it suggests, and save the SUR file again.
One caveat!! - I understand from reading other peoples' posts that FL Model Tool doesn't handle models with break-off components? I don't know, I haven't made any so far. So be careful not to lose your last copy of your model .cmp or its .sur file.
But this method worked for me a couple of times when I had similar problems.
Such annoyances, but such a quick solution, so many thanks to the mentally far-superior-guys who investigated over months (if not years) and wrote these utilities, please keep them coming lads!!