Just wondering if this odd gap problem may be to do with the Stations From Beyond mod or if anyone has experienced this in a purely vanilla game.

What generally happens is that some vertical hatches don't allow water to pass through them, it's like the two outpost modules do not have gaps set up correctly for the water to flow between them, so there could be a fully flooded room (module) connected to a room (module) below via a hatch, but when the hatch is open no water floods down through it.

At the last station I was docked to this occurred between the station and the submarine (the docking hatches), and also one or two regular vertical shafts / hatches.

I'm hesitant to disable Stations From Beyond in case doing so would corrupt my current campaign save (I suppose I could take a backup of the save file though).