Flight deck poles disappearing

I'm trying to make a realistic aircraft carrier mod, and it's done other than a couple of weird problems with one of them.
I've given the carriers realistic armour levels acccording to historical info, which works fine, except for the Glorious.
She's set up like a battleship originally, but when i reduce the armour levels, just before she's had enough and is ready to sink, the 6 poles that stick up from her flight deck, drop through the deck and disappear.
I can't find any clue as to why this occurs, but i'm sure it's not supposed to.
The other problem is that she was a flotation zone short at each end, which caused her to nose dive when damaged forward of the engines, so i added 2 zones, and spheres for them. Problem was that when she got hit by gunfire it would set off a series of explosions, blowing off the guns, planes, cranes and even the funnel and bridge assembly. In fact the funnel and bridge would disappear through the deck like the poles.

Does anyone know what might cause these problems?

It appears to be related to the spheres, because just adding the zones doesn't result in problems. But i need to have spheres to register collisions to the zones.
I've not had this problem with the other carriers, although the spheres for the others covered the full length of the ship, so i'm a bit perplexed.

If i can sort this the mods ready.