encoder phase shifts

I am struggling to get a Yaskawa motor to work with a Rutex step/dir
to +/-10v controller. I can get the motor to move in one direction
only using Mach3 and a Campbell breakout board. I can move in the
other direction when I change settings on the amp and I can move in
either direction when I place a + or - voltage to the amp. I know the
motor is ready to move, but the Rutex does not like something. I fear
it may be the Yaskawa encoder.

My question is this: what do common encoders do with the phase A and B
when the direction is changed? In this situation the phase B preceeds
phase A by 90 degrees during forward motion and phase B lags phase A
during reverse motion. Perhaps the Rutex does not like this. I am
afraid that normal encoders do not shift the phase relationship with a
change in direction?

Thanks,
Keith