I think your problem lies in putting any water at all in the cannister. Any water in the can prevents the priming pump from operating. With the can empty the primer pump can start water flow from the intake tube, filling the can as it pushes the air out the exhaust tube. Any water at all in the can sets up a "vapor lock" in the circuit. I know my Fluval operates this way, and reading the owners manual on your Eheim (online), it seems to be the same........no water in the can at all at initial setup/startup nor on any subsequent cleaning re-starts. Try that next time......let the priming pump do it's work: prime the can.
Fluval Osaka 155
Fluval 306 Cannister - GLS Primo CO2 In-Line Injection - Kessil A150W Pendant LED