Your plot does thicken.
I am no diesel mechanic
or expert, and I am sure others here will have much more experience with diesels, but as I understand it:
A boat may have a small "day tank" that is used to hold prefiltered fuel and is usually near the engine, perhaps in an engine room. The day tank would or could be filtered multiple times before the fuel hits the engine. The purpose being to have a pre filtered "clean" source of fuel ready for the engine.
A larger fuel tank, possibly contaminated by water, possibly by human error when filling the "water" tank at the dock
, or by some other water ingress, would be separate from the day tank.
Note! People have been known to accidentally fill a fuel tank with water, by mistake, and the opposite too. Some boats have flat deck
fill plates that look very similar or even identical. A good thing to do on a new to you boat is to clearly identify all filler caps and clearly label them, so anyone can know what they are for, as others may be servicing the boat without your observation.
The boat could be used for a short time or the motor
started using the day tank, as that fuel may have been untouched by the water, and of sufficient quantity to start or demo the engine, or motor
for a while.
I hope this helps you. I am sure others here can offer more details or experience or suggestions.
If your investigation finds the cause, I hope you will report your findings as it may help others, including me. I come here to learn from the good and bad experiences of others.