The game is really good (I will certainly post more ideas after)
As for the leak problem, here is my 2 cents:
I think that the problem is that the possibility of the air leak is handled by tile and not by base.
For me it should (after some random times) see if the base have a malfuction, and if yes then a random tile belonging to the base should leak. Right now it seems that every tile is handled separately, so more tiles involve more dices rolls that could cause problem.
I also noted between two computer differences in the feeling (gameplay), Like the timer would use the time that has passed and not the number of frame elapsed (which means the game has a different feeling depending of your fps)
In any case, this is just my opinion/feeling, not actual facts.