I would suspect one of the following-
A) The power connection at the pump junction box (where the power and controller connect to the pump) is loose or poor. This could be because there is tension on the cord, for example the power supply or block is hanging in the air unsupported and there is a weak or intermittent connection. It may also be at some point the connection got wet, it only take s a drop of water to quickly corrode the connection, it can be ruined as easily as an unintended drop in the sump or a puddle of water. Check the power connection for any corrosion, it should all be bright shiny, nickel plate.
B)The pump is new and somewhat stiff, it has not worn in and may have some vaseline residue from a dry factory test run, as a result at low speeds the resistance is too high and it stops, try a higher speed for two weeks. Lately the factory has come out with the following break in recommendation for the 6055- 2 weeks at 18V with no pulsing. Not that any pulsing or higher or lower voltage hurts the pumps but they will wear in quietly and trouble free this way. You won't have the stopping of lower speeds or the louder noise of higher speeds.
C)The controller connection is loose, check that all cords are firmly connected, power, controller and power cord from the wall to the transformer.
D)Double check the controller settings, make sure that it is indeed in pulse mode and no other modes are on, such as wavemode or storm mode which may cause the pump to shut down as part of there normal operation.
