I promised Bill and Duane I would post a summary of the problem and have changed the subject line for better results in searches. I emailed Duane rather than posting, hoping to sort things out instead of having a flurry of back and forth posts and bounced ideas off of Bill while we were confirming the problem.
When I saw Duane's post evolving I emailed him to suggest a possible cause--a slow (bypass) leak from the desalination 3-way valve between the freshwater to the saltwater systems and offered a simple test: observe the water level in the strainer with the seacock (sea intake ball valve) closed and the fresh water system pressured up. If it rises over time--even slowly--it is a problem. Even with a very slow leak it will continue to push water into the sea water manifold. It seems that the generator loop is the way out for this water. The diesel engine raw water loop (fortunately) and the desalination filters are higher and for some reason the water does not escape through the AC loop (I am guessing it has something to do with the way salt water is selectively diverted to the 3 AC units). Of course, if the seacock to the strainer is open (either on-land or in the water) pressure will not build up and cause a problem.
I had had the same problem but happened to catch it quickly as I was trouble shooting for the source of the fresh water leak. Because the bypass leak can be very, very small (and still cause major problems over time) it can be difficult to detect by noticing excessive freshwater pump cycling. Like Duane, I had heard my fresh water pump cycle just once in the middle of the night. Also, difficulty cranking the generator can be a sign of a full lift muffler. It is probably only after the muffler and exhaust hose fills that water will back into the generator.
The problem is solved by installing a new 3-way valve. I am sure that Dessalator and Amel used a good valve, but after 10 years of exposure to salt water, a bit of electrolysis, etc, and perhaps lack of being worked it can develop a very slow leak that potentially could lead to a very big problem. I think that 3 way valves may be more susceptible to these kinds of problems than 2 way ball valves because the openings are closer.
I did not post at the time because I thought I had just made a procedural error. I have a 2 way ball valve between the salt water manifold and 3 way. Had I closed that during non-use of the Dessalator there would not have been a problem. I have just learned that it is not standard on Amels. I would, however suggest considering the valve and it is pretty easy to add if you are replacing your 3-way. If you have a leak in the filters or somewhere else in your desalination system you can still operate your engine and generator and it is handy when working on your system. It also prevents a potentially expensive problem if the 3 way valve develops a bypass leak over time. Occasionally I will forget to open it before making water but immediately see no low water pressure--I always look for this because I am also checking to make sure the low pressure feed pump is operating. Checking the oil in your generator before every operation is not a bad idea.
Bob, KAIMI SM 429