Glad to hear it's working out for ya!
Don't worry too much about it, in spite of what these naysayers will tell you, SH4's digital distributions (Yes,
that includes Steam!) aren't any less stable than retail versions once you finally get them fooled into working.
Oh, and as I recall, the CO2 shenanigans primarily happens when you shell back to the OS with Alt+Tab, though I'm open to correction on that.
There's also no 'fix' aside from a save/load as far as I know; some people will have it happen consistently, while others never see it at all... A strange issue, but not a game-breaking one IMO. Now get back to sea and give that enemy shipping hell!