Check all the grounds on the engine and chassis to make sure that they are good and solid without any corrosion.
I would also put a digital voltmeter on the engine and check the reading (at different rpms, including the ranges that you are noticing the problem) to make sure that you're not getting any surges or drops in the voltage. That kind of surging/drooping of the voltage usually triggers a check engine light because it will make sensors seem bad, but there is the random possibility this could do something like that. Don't be too concerned if you see between 13.5 volts max and about 11 volts min.
If everything looks good you could try changing the VSS (Vehicle Speed Sensor) and see if that fixes your problem. It could be just that it is getting a faulty signal and/or catching some odd interference from the voltage system.