I think this may be the problem
Sounds like your system cannot overcome an air lock when you loose prime.
Did you say that it happens more often when it's rough?
I'm thinking that your pick-up is sucking up air during rough weather and causing the air lock (similar to backing down at the bait barge)
When you open the washdown spigot, you allow the air bubble to move in the line and the pump re-primes itself and continues to pump.
I've heard Mark Wisch recommend to make sure that the bait tank inlet hose is routed to always run down hill to the pump(non-self-priming type) to prevent airlocks.
...or you can run one of these on your transom.
Not real pretty but these will never loose prime