Hi rayond6751,
I did have some MODs loaded, (which I shall list later), but as you have suggested, I have disabled them one by one, and exited the game between each.
I still have a crew playing fighter pilot, and a gun I am unable to aim.
I have only played "CAMPAIGN".
"MODS LIST"
a. NewUIs TDC 7 4 2 ByTheDarkWraith.
b. NewUIs TDC 7 4 2 jimimadrids map tools.
c. RedCapTools 0 2 alpha.
d. No Damn Bubbles, No Damn Halo Mod.
e. Enhanced Ship Recon Manual V2.10.
f. EQuaTool 01.01 by AvM - Large Style.
g. Equipment Upgrades Fix v1 4 byTheBeast.
I hope this is of some help.
Having to point the sub at the target to shoot them is getting a bit dicey.

I am hoping that I wont have to restart the game from the start.
ATB
Gary