Originally Posted by c640947
I do not believe it is the check valves (good thought though) as the pump does not turn on. Check valve issue would be pump is on but not moving water i think.
Since all 3 pumps are affected, both directions, and it comes and goes, I vote the ground or power wire to your relay box is loose. All three relays (I believe the 06 has no timers but does have relays) likely run off of a single power wire and ground wire from the battery on/off switch to the relay box. Make sure to check both ends of the power and ground wires to the relays and good luck.