Look in the skimmer. If the water level is too low, you could be creating a whirlpool, like the last bit of draining a bathtub, where air can get sucked in. Or, the flapper -"weir" is the proper term - could be binding. This will cause the same effect in the skimmer, until the pressure from the pool forces it open, and it floods, and the problem is solved for a minute.
Also, is there an air bleed on the filter? If so, crack it until water shoots out then close it up. Could be air trapped which can cause essentially water hammer like you sometimes get in the house plumbing.
And Jason types faster than me.
Rereading it, it could also be a soft hose collapsing. You might need to put a section of pipe in there or replace it with a stiffer hose.