what are you using as a co2 diffuser? a reactor, a ceramic disc diffuser, ....? could be some sort of blockage somewhere. try removing whatever that you are using as a diffuser and check the flowrate.
you get co2 bubbling better in the bubble counter when you unscrew the bubble counter slightly due to co2 being 'allowed to leak'. check if the co2 flowrate becomes 'retarded' again if you tighten the bubble counter again.
it is normal for tank water to flow back down the tube towards the co2 cylinder. this is caused by co2 being absorbed into the water.
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