After digging around I have found a really simple method to fix the problem of the deck gun crew slots disappearing.
Simply open the ActiveUserPlayerUnits.upc file in a text editor, and remove all instances of "AdditionalRepository". I was able to do this with 1 easy find and replace command. The file can be found in the SH4 folder in your documents. ../SH4/data/cfg/SaveGames/*/ActiveUserPlayerUnits.upc
What you are doing is changing the lines like:
[UserPlayerUnit 1.Compartment 9.CrewMemberSlot
AdditionalRepository 1]
to read.....
[UserPlayerUnit 1.Compartment 9.CrewMemberSlot 1]
simples