Changes made for Pathfinder 5226 controllers.

The magnetic memory on a 5226 board is used to save things like reference state and encoder counts when the controller is powered down. One fault with this is that if the wrong machine type was chosen with an incremental encoder it will save the state of needing to be referenced. If the correct type is chosen later without an incremental encoder that machine type has no way of getting the needs referencing state to clear.

The solution was to clear the referencing state at startup if the axis does not have an incremental encoder.