Is everything in, around, and under the pool bonded together, including all electrical devices, per NEC? Galvanic action can set up some pretty good currents. Do you get the problem when the power is off to the lights?
One side of their LV x-fmr (or the center tap) should be tied to ground otherwise you can get a floating voltage that can be very high, especially if there is a problem with the windings in their x-fmr. (Don't change their product, just investigate) Is the x-fmr listed for such a use? I have found many in the past that aren't...