I don't know if I can be of too much help= I've been away from the Pacific and TMO for a bit. Been spending my time lately in the cold, grey Atlantic with SH3, but....
IIRC, there has always been a issue with the fore and aft deck guns in SH4. I believe Ducimus states in TMO to choose one or the other and stick to it. I can't remember if picking both causes issues or what. I think he addresses it in the TMO manual and I seem to remember a file you have to pick depending on what configuration you want.
I'm sorry if I can't be much more help and it is very possible I may be blowing smoke out my you know what.
I'm sure someone may be along shortly that can provide a much better answer.
Welcome aboard!