I would be inclined to think that what you are seeing is water hammering of some form. There will probably be a bend in the plumbing that has air trapped in it. When the water is being pumped through the system, this compressors the air. When the water is no longer being pumped - the air expands back out to its normal volume, it can be quite energetic and I have seen it burst pipes in residential plumbing applications.
Since it is a new pool, there is a possibility that a pipe that was straight became bent during the winter. The depth of the bend just needs to be greater than the width of the pipe in order to trap air in an otherwise straight pipe. That will be enough in order to form a seal with water before all the air is evacuated from the pipes.
There are a lot of methods of removal - but chances are pretty good that if you let the pump run for a couple of days non-stop it will take care of the problem on its own. Moving water is really good at dissolving air into it.
Regarding the valve switched to floor drain and still getting blow out from the skimmer - as I understand it, the current plumbing runs a secondary pipe from the skimmer to the floor drain in order to prevent a low water level from causing the skimmer to loose suction and burn out your pump. That would allow the hammering to continue if the air pocket was on the main drain line (might check to see if it still hammers when you have the valve set to suck only from the skimmer).
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