I get a similar issue while in the pens or inside the sub.
though this almost never occurs inside the command room, other parts of the sub are prone to this experience.
I'll enter the area of the captains bunk / sonar / radio area...
sometimes the whole screen will go dark. Then after 3 to 5 seconds (rarely longer than 10 seconds) everything will fade back in from black.
strange, annoying... i have tried various graphic options changes, also updated drivers.
nothing seems to fix this.
only once has the game not recovered from the black screen.
Inside the pens... i seem to notice this issue right after the lights flicker off. for a moment.
the lights dont actually go OFF but the glow of light cast upon surrounding objects goes away... then sometimes immediately afterward i have this black screen problem.
99% of the time though it fades back in to normal after a few seconds