It was most definitely the flush valve at the watermaker pre-filter. I verified it this way:
Do this overnight so there are minimal other factors such as use of the freshwater system.
1.On the hard so no ocean to complicate things
2. Empty seachest and remove seachest lid
3. Close seachest thru-hull valve and leave the freshwater pump ON
4. Ensure watermaker flush valve set to provide seawater to watermaker
5. In the morning if the seachest has freshwater in it, the flush valve is leaking. Mine was half full in the morning.
This will also work if you are in the water and are sure the seachest thru-hull is not leaking. You could empty the seachest and wipe it down with freshwater (so you can check the salinity) to be sure. For a double check, the next night do the same process but in #3 leave the freshwater pump OFF. If no water the second night you are absolutely sure it's the flush valve leaking.
I will be adding a ball valve between the freshwater pump and the watermaker flush valve. There is no danger from the freshwater leak thru the watermaker flush valve as long as one of the following conditions are met:
A. Seachest thru-hull valve is open (any freshwater pressure will go to the sea before the genny), or;
B. Seachest lid is removed so the freshwater leaking past will spill into the bilge (recommended if you are hauled out and living aboard with the freshwater pump on).