Even during the day they don't pulse? What should happen is in day mode the pumps pulse, in night mode they stay at one speed. I would check this by feel more so than sight.
I see three possibilities.
1) If it pulses during the day, and sets to one speed at night and the speed is just the higher then the speeds need to be reversed.
2) The pump is not responding to the controller at all, the most likely cause is the cable is bad or not fully inserted.
3) If nightmode is on all the time during the day, this would be shown by the moonlight running when the lights are on if moonlight is turned on. The photocell may just be upside down, there is a side with the photovoltaic grid and one with the wiring running underneath, the photovoltaic grid must face toward the light.