The pumps and electricals should be inside the portside storage area against the inside of the hull. They should have resettable circuit breakers, I believe there should be 6 breakers. 2006 should have been the first of the impeller pumps. The impeller blades could also be gone causing them to fail to drain but the scoops will allow them to fill. I suppose it is also possible the 2006 could have been an early boat with the aerator pumps like my boat, If it has knobs at the helm for valves it's the old system, no knobs near the driver's right knee then it's impeller pumps.
Nick is correct there should be a 2 bosch cube relays for each pump, 1 for fill, 1 for drain. They should have individual circuit breakers for each relay. A bad relay or a bad/tripped circuit breaker can cause what you describe. I am not a fan of this ballast system as it is prone to lots of failures if you don't watch is very closely when draining.
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