If indeed your problem was caused by the anti-siphon being blocked -- this is yet one more reason to close your intake through-hull when the engine is not in use!
MV DANA LOUIS said:
If that tube is obstructed [in our case by an insect family], on diesel shutdown the tube cannot break a vacuum in the exhaust loop and seawater is sucked back through the exhaust riser into the diesel. You know this has happened when you try to start and get almost no turnover [water does not compress] - or, if you are really unlucky, an engine that starts up on 3 cylinders and mangles the valves, piston etc in the cylinder with the water.
This makes me wonder why you didn't mangle any valves, etc given how long this problem persisted and how many times you started the engine!? One way to find out whether your water lift muffler was backfilling would be to take a good look at it and see if it's over-full of water? If it's not, I doubt this problem was caused by the blocked anti-siphon line (which may not have been 100% blocked, it only takes a tiny bit of air to break the siphon).
Another possibility is that the boat got tilted excessively while being hauled out or re-launched, which can cause water to flow back from the water-lift muffler into the head. I know of at least one instance where this happened, resulting in a re-build.
One point of correction to the warning posted by the MV above: The raw water in the water-lift doesn't actually get sucked back through the exhaust riser, it merely back flows by gravity when the water level in the exhaust system reaches a point where it exceeds the high point of the elbow.