I have had the same problem with my glass plate diffusor. All you have to do when you lower the reactor is to wait for the gas to bubble again. It should shortly bubble, but in your system it might take longer since it's going at 1 buble every 3 secs. I am not sure of the exact reason for this but I think its due to increased water pressure. Just wait for the CO2 to build up pressure enough to counter the water pressure pushing against the tubing.