Could it be that the pump isn't pumping up enough water to fill the top fast enough to compensate for what is flowing down? So, there's a surge of water when there's enough water built up?
(I honestly have no idea...I've never had this problem...and I don't mess with plumbing. Just a guess.)
Oh, I also had something similiar happen...there was a snail stuck in the plumbing that was blocking the water...until the pressure was high enough, the snail was moved by the water so the water could pass...the snail would upright itself...and repeat.