I've never found those glass non-return valves to be particularly efficient. When your CO2 comes on again in the morning it should push the water back up.
The point of the non-return valve is to stop water reaching your regulator (which would damage it), so if you think the water is going past the non-return valve get another valve - you can always have two inline, so you can keep your existing one and put an uglier cheaper plastic one between the current one and the regulator.
That kit works great once you've got it set up and working, so don't give up.
Mark
PS do you have a solenoid, or or you running 24 hours, or are you trying to turn the CO2 off manually at night? The regulator with that kit is only really suitable for the first two options, as you'd have to reset the bubble count every day, and it would never be the same.