I have noticed a similar, but much weaker pulsing tendency, when I connect a 36v battery while the controller is still programmed for 24v.
Have you tried setting the controller to 36V and using the 24V battery?
This won't work with later MP4 or MP5 controllers because the 36V low voltage setting will be too high for a 24V pack but it may work with your MPIII controller.
I looked through the "Voltage mode pedelec sensor" thread referenced, but does not that option also require installation of an accessory Cycle Analyst?
The Cycle Analyst allows greater control over the Pedelec sensor signal output, which means it can be fine tuned to suit the rider, but The Voltage Mode pedelec sensor should still work OK without a Cycle Analyst if wired directly to the throttle signal wire.
If the output signal from the Voltage Mode sensor was passed through a suitable variable resistor
(probably 3-5KOhm) it should be possible to adjust
(reduce only) the assistance relative to the pedal rpm.
More magnets could be added to the magnet ring to increase the assistance relative to the pedal rpm.
Alan