You can, if you wish to, leave that first option for Carbonite checked. Go to the default Blizzard key bindings, and in the Carbonite section you can set a key bind (I use "alt + m") to open the Blizzard map (I think it's says "Open original map", or something to that effect). That way when you hit "M" the Carbonite maximized map will open, but if you hit your key binding, the Blizzard map will open.
Also, as far as I can tell, with Carbonite's map as long as the "Hide in combat" check box is not used the Carbonite map stays open during combat. Obviously, though, checking it will force it to close during combat. I have absolutely no idea how you would get the Blizzard map to use this behavior.
"I have disabled all other addons and believe this to be an issue with how carbonite controls the toggle of the map. In fights this command is somehow disabled."
But have you tried this with Carbonite disabled? That is the only way you can get an accurate answer. Try disabling ALL addons and see if the same thing happens.
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