C,
Looking at the pics, you can see where the wiring going to the pump and the wiring going to your light controller are all crammed together and touching each other.. This is not an issue for the electricity, but it does allow noise to jump from one wire to the other..
You can try to rearrange the wires to separate the power going to the light controller from the other wires. It may or may not help, the only way to know would be to try it.
I suspect that a simple noise filter will fix your problem as has been stated above.
Thanks,
Jim R.