Just how deep was the water you ran through? If you stop in water that covers the tailpipe, the car stalls and can't be restarted due to backpressure on the exhaust. This can happen without water even coming close to ingestion into the engine.
Is there water in the oil? This might be manifested by milkshake-like appearance of the oil, and could shed light on the depth of the problem as well.
I've heard of brave souls simply removing the spark plugs and cranking the engine to expel water from the cylinders...
Anyway, I tend to agree you're being fed a line. Give us some more background if you can.
