Disclaimer:
I don't own this game, I just helped a friend who has had some trouble with this boat.
He is more the gamer, I more the builder....so here we go:

After some heavy storms, the auto-ballast--system stopped to work.
After it has emptied it's ballast-tanks, there was no way to refill the tanks anymore.
Even after disabeling the auto-logics.

I solved the problem with fluid-filters.

My guess, what might happened.
During the storm, the boat was sometimes flying in the air and even capsizes multiple times.
The ballast-system was active at this time.

So it might be, that the systems sucked in some air instead of seawater, and the air was stuck in the pipes because of still water at the other side (the ocean or the tank).
So the ballast-tanks were stuck at 0. (air cannot go into ocean water).

I am just guessing here, but this seems to be a game limitation, which might cause this issue.

So in short, never mix fluids within a piped-system.

The only soultion I found so far, are fluid-filters DIRECTLY after the water-intakes (fluid-ports).
So far...the system survived two more heavy storms....
I guess all your other boats are affecetd by the same (game-engine-related)problem.

Otherwise...you are making nice boats....A lot of interesting stuff to play around with...