First thing to check
Timsail,
I have this problem from time to time on my B361. When sailing in rough seas, the raw water line drains and loses its prime. So, make sure your through-hull valve is open and that water is flowing to the A/C raw water pump. My hose to the pump has a small seacock right under the pump so that I can bleed the air out of the line. I hope yours does, too.
If that is not the problem, you may have a problem in the electronics that is not telling the raw water pump to kick on.
Agaliha