AKD, actually it was the \My Documents\SH4\data\cfg\GameplaySettings.cfg that I was editing, now that I check
It contains these entries:
[Current]
LimitedBatteries=true
LimitedCompressedAir=true
LimitedO2=true
LimitedFuel=true
RealisticRepairTime=true
ManualTargetingSystem=true
NoMapUpdate=false
RealisticSensors=true
DudTorpedoes=true
RealisticReload=false
NoEventCamera=false
NoExternalView=false
NoStabilizeView=false
MPShowPlayerNames=true
MPShowTorpedoes=true
[MiscSettings]
MeasurementUnits=imperial
These look to be the same ones you can set up in your office at HQ. No matter what I did to this file though, the changes were always undone as soon as I loaded a saved game.
DH