I agree it could be getting in the cylinders. I have had a small crack on some old camel hump heads right in the intake valve seat. The engine would run fine but did loose water. I too ended up filling a cylinder with water. A sign that water is getting in the cylinder while running is if you pull your plugs the one that has water getting in there will look brand new. When I pulled the heads I found the cylinder the water was getting in had a very clean piston and the combustion chamber in the head along with valves were very clean.
Like said above I hope it's not your problem and of course check the simple things first.