I had not thought of the possiblity of phasing like when you watch a wagon wheel on tv.  I suppose that's possible.

The shaft is turning in the ten to one hundred RPM range, directly on the shaft of the floor chain idler.  The other shaft is turning at a similar speed on the augers, and it works.  Apron chains are the type of application they were intended for originally.  The encoders have one digit different in their part number, so possibly they have different numbers of windows in the hall effect wheels. 

Would just supplying 12v to the sensor power wire be a good, bad, or neutral idea? 

I wanted to switch channels and see what happened, but we took it to the field running on manual, so I don't have the option to mess with it right now.  What we have now is a whole lot more defensible then running with no meters at all and two water valves to control the hydraulic flow, like we did for a few days late last year!