Having issues with part scaling in Ship Designer

So I've been away from the game for a while and have started to play again.  This time creating my own Civilisation and with that come custom ships.

I've started to design only a couple of ships at the moment (a small scout, a dreadnought on a huge chassis).  The scout is fine although I'm probably gonna scrap it because its terrible.  The Dreadnought on the other hand I very much like where I'm going with it (I play Firestorm Armada, some may recognise the shape from there).

Currently I'm saving progress as a ship template in the designer everything looks fine (see above), however when I load the template into the faction fleet style screen some of the parts scaling are way off.

Any idea why it's doing this? Any suggestions are gratefully received.