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For clarification, is the latest red graph showing the voltage from the sensor or the number of pulses over a time period?

I'm trying to establish whether the 'noise' is really random variations in signal or whether it is showing the wheel stopping in the same place repeatedly.  The unknown in this is how the flow is detected, does the mechanism, which I assume is an impeller, have any preferential stopping points (cogging for example) or can it stop freely at any angle.  How many pulses per liter does the unit produce? For example does the graph show three rotations of the sensor wheel or are some hidden in the sampling period.

A side thought, assuming your water usage never varies much from average, can you use a monostable (in software or hardware) to block any signal faster than your maximum usage.

Brian.