That sounds normal, my bubble counter does that too, the last bubble sometimes just sits at the counter nozzle and then slowly disappears. Its just from the change in pressure as the Co2 gets used up in the tubing and diffuser.
Do you have an additional check-valve installed between the bubble counter and diffuser? That will help prevent tank water from flowing back and mixing with the bubble counter water.
Its also normal for the BPS to be a bit faster when the solenoid is switched on initially every day, thats because the tubing and diffuser doesn't have any Co2 pressure at the start, so the initial gas injected has an easier time to fill them up. Once the pressure builds up within the tubing and diffuser, then the BPS will settle to a more consistent rate.
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