Try the commands 'Decks awash depth', maybe this will run with electric engines too, i don't know.
You have also manual control of the dive planes, try it out, maybe your sub is not entirely on the surface.
You can also command your engineer for better flooding managment.
If still you are stucked, I recommend you make a save/reload, this will at least make game malfunctions go away, but normally you wouldn't save game in these conditions.
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