Hi,
Im using an Eheim ecco canister, I have the same symptoms everytime I start the canister. If Im not wrong the knocking sound is caused by the ball valve vibrating which is normal when water starts to flow in.
For the reason that it stops sucking water after awhile is when the canister is full, but the circulation of water stopped because the siphon cycle is incomplete. One reason being the motor of the canister is not strong enough to push water through the outlet. I guess your canister is placed either far from your tank or the tank is places very much higher than usual. Then laws of gravity comes to play.
Try this, empty the canister of water and start it. When you hear the knocking sound and water being suck, lift the canister up to either to level with your tank or higher which is better. Once you see water flowing out of your outlet, the siphon cycle is complete. Then you may place back your canister in the position you want. You have to do this everytime the canister is turned off.
If this fails then I think the canister may be faulty. Gook luck bro.
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