I have finally fixed this problem, and I will share my story with you so that if it ever happens to you it can be fixed the first time (it took me multiple times and a number of months).
I own (or maybe it owns me) Pandemonium, a Beneteau 323 in San Diego. This is a pretty good situation almost all of the time.
However....
About 4 months ago my engine, a Yanmar 2GM (2 cylinder), started acting up by not circulating raw (salt) water through the engine. Not good as the engine will overheat pretty quickly without the water circulating (note that my overheat alarm works well). Sometimes it would work OK, and sometimes not. Sometimes OK when I left the dock and not OK when I started the engine to return. Seems that there was an air lock at the raw water strainer. You will know if this happens, the exhaust will sound like a motorcycle. What to do?
First, and most obvious, fix is to check the water pump and replace the impeller. This was done, and everything OK for a couple of sails. But the problem was still there. Next thing is to talk to our local Yanmar dealer (who is very good) to get ideas: Nothing. Finally a chance remark by one of the mechanics working on the boat led to the actual problem. He commented that the raw water strainer was rather high up, which he thought was unusual. I know why Beneteau placed it there: that is the only place for it in the engine compartment. But it is difficult for the water pump to get the water up hill and the pump is not really self priming. Healing over when sailing tends to cause the air lock, especially on starboard tack.
Finally I discussed this remark with the repair company manager (also very competent and experienced) and he said that it was unusual to have the strainer that high. So I requested that it be moved lower, as low a possible. Done, and problem fixed. The salt water now has an almost horizontal path to the pump on the engine (through the strainer).
For B323 owners, the strainer ended up in the aft cabin space just behind the engine where the shaft exits the hull. The mechanic had to install a small piece of wood to make a place to attach the strainer and re-plumb it with new hoses. Not a big job at all. This also has the advantage of making it very easy to check the strainer and clean it if necessary.
Hopefully you will not have this problem, but if you do you now know the fix.
Fair winds,
Paul
"Live long and prosper"
Mr. Spock
Paul Nierman
B323 Pandemonium