OK, I have the spindle encoder plugged into the Y input and it is working.
I still have the Jerky stepper motor problem with the standard SyilAmericaC6 profile.
As I mentioned, I can rapid in Z but even with Z when pressing the Jog arrow I get sporadic reversal of direction.
No Rapid at all on the X axis, and very jerky jog.
I use the same laptop for my Sherline and it works fine, so I know the laptop is fast enough for Mach3.