With most canister filters, if there is even a little amount of air in the pump chamber it cannot start a proper siphon.
Most of the newer canister filters are equipped with a priming mechanism, usually in the form of a hand pump. You prime the canister first to make sure there is no air trapped and then you start the filter.
On my old canister filter, the only way to prime the canister after cleaning it was to start the filter for a few seconds - just enough to get water sucked into the overflow and then turn the unit off.
I then wait for the water to flow into the canister and completely flood the chamber. And then I start the filter again.
If you also have a bad seal on the canister cover or the intake tubes, this could also prevent the canister filter from working properly as it could be sucking in air into the canister while running.
When your canister filter runs, can you hear gurgling or can you feel any churning within the canister?