Hey there, jimmbbo! Like ETR3(SS) says, the Save of the game, exit the game, re-start the game, and reload the Save will clear your CO2 level, and hopefully will clear the red markers. Are you seeing a bunch of "ship sunk" icons? Or red triangles for airplanes, or red squares for ships, or all of the above?
Your first issue is usually caused from "shelling-out" to Windows, either by use of the <Ctrl><Tab>, <Alt><Tab> or <Windows> key combinations. If you need to leave the game, it's best to Save and exit the game. None of the Silent Hunter games are compliant with a 'modern' Windows OS, as far as audio streaming and other 'modern' features of a newer computer go. In other words, the game does not release the resources it is using, and Windows assumes it does, so takes back control of those resources. When you go back into the game, Windows gives the resources back to the game, but with different "addresses" of where they are, and the game then "loses its place", if you will, and can't find where it was, so kind of stumbles along with what it has, resulting in quite a bit of weirdness.
The second issue might be related to that, but what can also happen is if you are using mods, and load Saves. As an example, say you activate a mod, play the game to check-out the mod, then Save the scenario you're in for later use. You then de-activate that first mod, and either play Stock, or activate a second mod, and you see that first Save and want to try it in the new set-up, you might find that the Save is no longer compatible with the game the way it is now set-up, resulting in a game that runs, but has all sorts of strangeness about it... You cannot use a Save from stock in TMO, and you cannot use a Save from TMO in stock. You have to keep Saves in their original "environment".
If you like to check-out several mods, look into using
MultiSH4 (download link) to create new Save folders for each copy of SH4 you use. There is also a
Release thread for it.
