This one has me stumped...You would/should be getting a hydraulic lock on the engine if it was comming through the exhaust valves and some serious rusting as quickly as over the week end it being salt water...
Water is not usually going to flow by your piston rings that easily and most will remain in the cylinder.
Are you getting any excess steam out the exhaust while running at normal temp?
If the inline exhaust valve cures the problem 100% all the time, then it dose point to that issue but this will be a new one on me as far as it ending up straight into the crankcase with out signs of hydraulic lock.
Re: your question on if it could becoming straight into the crankcase from the heat exchanger... my answer is no...as the only place it mates with the block is at the exhaust ports on the head...more common would be raw water/ coolent contamination in that case...I supose its possibal to have a crack in an exhaust port alowing water into the head and block but I would think you would have exccisive back pressure out the crank case breather if that was the case as well.
Plain raw sea water in the crankcase could come from several places if you were raw water cooled but is really isolated to down flooding as you summized already with a fresh watewr cooled system.
How does this engine Start?....and run?
Is there blue smoke?
Its possible to have say enough scoring/dammaged piston and rings on one cylinder or its wall to allow some water past the rings but we are talking rebuild ready condition here for that to be the case..blue smoke, oil consumption all that jazz...Water is less solvent then oil so it really doesn't seep past rings that readily.
Like I sad this one stumps me a bit from all my past experiences.
Engines are always teaching.... Im always learning..