Hm, i had a similar problem when i've done a ship for "Flottenbasis Kriegsjahr" campaign. It is made from the files of german "Blockadebrecher", bridge from aux cruiser and so on.
Because of that the german ship has to many mastnodes, ive deleted some of them by setting the ID for geometry and material to 0 and then every time when the ship was breaking sh3 crashed.
To make it somewhat shorter, their were SH3ZonesCtrl for all mastnodes named macara in zon file. After deleting of not used one all was fine.
Maybe that helps to solve your problem.
And merry christmas!
