This is curious but the system has basically a suction side (thru hull --> sea chest (including the manifold for the toilets/AC etc --> transmission intercooler --> suction side of the Yanmar engine driven sea water pump including the pump cover), and the pressure side (i.e. output side) as you know goes from the pump to the engine oil cooler --> to the engine coolant heat exchanger --> to the turbo exhaust elbow --> etc.
The output of the pump is dependent on there being both not too much suction required, and not too much head of pressure to pump against. In this case I would guess that you have an air leak on the suction side in combination with some sort of (perhaps relative) obstruction on the suction side. Or, less likely in my opinion, there might be an obstruction on the outflow side (most commonly due to impeller pieces at the inlet of the engine oil intercooler). Once the pressure is reduced on the output side by removing the hose, water can literally "flow" and the suction leak is relieved as not as much suction is required.
My trouble shooting usually follows the path of least resistance, and here is how I perceive that:
1. Are you absolutely certain that the O ring is in the groove for the cover of the sea water pump (i.e. the O ring that seals the pump cover to the pump housing)?
2. While you are checking that, visually confirm the impeller blades are in good shape. You might even motor the engine thru a few cranks with the cover off the pump (sea chest closed) and verify the impeller is turning. I had one once that delaminated the rubber from the metallic hub and while the hub turned the impeller was turning at a different rate.
2. Have you inspected the transmission intercooler to see if it is clogged creating a suction side negative pressure that may be resulting entrainment air leak at any of the joints between the sea chest and the sea water pump inlet.
3. Have you tried shutting off the manifold to the toilets, AC etc to see if perhaps the air entrainment is coming from there.
4. Are you sure there isn't partial blockage of the thru hull, resulting in greater negative pressure on the suction side.
5. Have you verified that the inlet to the engine oil intercooler (tucked between the turbo and engine block) is clear (this is harder to get at so that is why I have listed it last.)
6. How many hours on the engine/sea water pump, I suppose if it is a high time engine there could be a water pump shaft seal leak allowing air entrainment. If all else fails swap out the sea water pump with your new spare one.
Just some ideas, let us know what you eventually find.
Gary S. Silver
s/v Liahona Amel SM 2000 On the hard for two more weeks Puerto Del Rey, Puerto Rico
Hull # 335