First the bad news:
I thought I had it completely fixed by editing the CrewMember IDs (I had no working systems at all), but it seems I'm still missing - just like you - a working flak system... Editing the crewmember IDs probably won't help you if all your other systems are working..
Now the good news:
I got a working flak system by replacing the Scheer's conning tower with the IXD2's. Unfortunately it messes up the Scheer's textures and something tells me the IXD2 conning tower doesn't quite fit here
At least now I know there must be something wrong with the Scheer's conning tower. My guess is something in the .cam or .sim file...
I'll try to solve it but this involves .dat, .cam and .sim editing and will take some time (if I succeed anyway).