Ah, I think I had somewhat the same problem. I did the fuse, generators, vodka, dials, and the radios. Then the submarine came up, so we went on to the foghorns. I'm think we did them incorrectly but the green beam light wasn't showing up, so I checked to see if the submarine was there still and it was gone. About 2 or 3 rounds passed and I messed with the levers and wheel for a awhile( I couldn't do anything with them because they were stuck in place), checked the lighthouse dials for correction, then checked the submarine again and it came back up. We attempted the foghorns again, in the same order we did before the sub went down, and got the green light!
What I'm thinking is that the foghorns sometimes change order so I just keep trying the same order until the submarines signal gets it at the order I want it to be.
*Honestly, I'm not sure if this solved your problem, but I hope it atleast helped ^^*