[aanker]

Yes it's a common issue, here's are some good threads that will help you fix it:

http://www.subsim.com/radioroom/showthread.php?t=222887

and Coletrains:
http://www.subsim.com/radioroom/showthread.php?t=121472

also neumanf15's:
http://www.subsim.com/radioroom/showthread.php?t=121460

Coletrains (post #14) in this thread:
http://www.subsim.com/radioroom/showthread.php?t=121472

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http://www.subsim.com/radioroom/showthread.php?t=222887
wolfeinsamer's fix for deck gun crew slots disappearing.
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.CrewMemberSlotAdditionalRepository 1]
to read.....
[UserPlayerUnit 1.Compartment 9.CrewMemberSlot 1]

At least we can fix it now. Usually happens if you change the gun from fore to aft or vice versa from where it was when first installed.

Happy Hunting!