They should have but I will try that first. If I still get the same problem then I'll just start again. The model is built, I just need to import the parts into GMAX, texturing as I go.
At some point I must have pressed a button by mistake as all the objects became sort of reversed in the 3D view. Not flipped, but FS5 quality bleed-through! Looked most odd and made it impossible to work.
I fixed that by starting a new project and Merging the whole lot back in. This didn't fix the Scaling thingy though.

I was able to do a quick export of the unfinished model by restarting the computer first.
It looks great in FS so I really hope this doesn't end up as an abandoned project. Only 4000 polys ATM, for me that's phenomenal, they're normally around the 50000 mark!
Kev