There is mention in the HAL of closed-loop steppers. Does this mean that you are closing the position loop in LinuxCNC HAL with encoders and PID (you clearly _are_ doing this) but do you also have closed-loop stepper drivers that also read the encoders?
It is possible that your problem is due to cascaded controllers.
I would be tempted to try a making an alternate config without the DPLL and with the stepgens in position mode, directly driven by motor-pos-cmd. Having a PID in HAL ought to give better results, but if the problem goes away with a more "classic" config then that at least suggests somewhere to look.
