Hrmmm, thats an odd one. do you have pressure gauges on the regulator on top of the cylinder? if so what do they read? the pressure in the clyinder should be about 1200-1300 PSI and the outflow side should be about 30 PSI. if those are right then you have plenty of CO2 in the cylinder.
The next question is how is the whole thing set up? Is the bubble counter attached to the regulator or is it further up the system in-line? if it is up further, is there a one way valve at any point to stop water flowing back up the system? are using the black hose? i ask becuase it means you cant see the water inside it. If water is flowing back up the CO2 tubing and down to the one way vlave then all that water has to be pushed out before gas will flow. I suspect thats what might be going on here.
If you have a one way valve move it right up behind the bubble counter so the gas/water interface is nice and close to it. That way when you turn it on the gas only has to force out a bit of water, not the entire tube worth.
My system used clear tube so i can see where the water is and the when they system is not presurised (my is automated so it turns on and off on a regular basis) the water quickly flows back up to the one way valve from the pressure from the reactor.
if not then give us an indication of how it is set up...e.g.
Mine goes clyinder -> regulator -> solinoid -> one way vlave next to the solinoid - (1 metre)> one way valve next to bubble counter - (10cms)> bubble counter -(20cms)> Reactor (external) -> CO2 infused water goes into the tan via outflow of one of the canister filters.
Hope that helps
Oh, one final thing, make sure you have a one way valve at some point, dont want water getting into the solinoid or regulator...bad news