I believe I can solve your problems.
For the turrets, do you have Turret=yes in their rules entries?

Also, make sure they're like tnkdtur.vxl/hva. Do it like that. I haven't had problems stemming from bad turret stuff. I'm almost sure something else is getting in the way.
[REPBO]
Prerequisite=SHIPYARD,RADAR
Um, remove the SHIPYARD. There is another source of internals. I tried doing the same thing and I got internals.
We still don't know when the internals occur? Do they when the unit finishes building, when you try to build it or while the game is loading?
If it centers around the unit, you fecked up the unit somehow. During loading, it can be anything...