Could be several reasons for this. After cleaning and re priming, be sure all the air is out BEFORE starting back up. Be sure all connections are tight ans clamps etc are tight. Eliminate droops in the lines, and be sure there is no way that them intake can suck air up.
I agree, it has to be sucking air from some place. Make sure all your fittings are tight on the suction side of the filter and the intake stays submerged.
Or it had air trapped in it from cleaning.
Wattsupdoc, that avatar gives me a chuckle every time I see it.
It can also be cavitation which is fairly common with canister filters.
Cavitation is caused by a restriction such as clogged filter media or a kinked hose.