Sorry but this is one thing you cannot blame on GWX 2.
Dead hampsters... check
de-magnetised fridge magnets... check
clicking delete on your save by mistake... check
these are examples on things that may legitmately be blamed on GWX 2. Not this issue though.
This is veyr much an "SH3 problem"
If this was your first patrol and before setting sail you upgraded the Sub that can lead to zilch by way of score.
Also if you changed anything mid patrol by way of MODS and such that can cause issue. Not having the GWX 2 cfg files installed in SH3 commander and so on...
There is a section in the GWX manual that explains in detail about odd game behaviour.