Ok, the code does not refer to how many times you press each button, but rather to the order. So, if I remember correctly, you want to press the middle button on the generator once, then press the third button once, and then the first button once. Repeat that sequence on the valves in the other room, and you'll light up the lighthouse... I might have mixed up the order there, but you get the idea...
But now I'm stuck again... I've explored the entire lighthouse, read lots of notes, looked at lots of pictures... but haven't found anything else to do! There is one door (Drake's) with some kinda code lock, but I have no idea what to do with that... other than that, all I've seen are some unresponsive controls up near the main light...
Hmm, so far this installment is proving much harder than the first!