Tuning EMC

I am now discovering the joys, and pitfalls of tuning a servo system.
There are two problems I have not overcome.

1) using frequency mod, I step one axis away from zero in 0.100"
increments and then back again, but it doesn't return to zero. there
seems to be some backlash<?> Each axis has a different amount of
error from 0.0009 to 0.005". If I keep stepping in the same direction
it moves 0.100 like it should. could the encoder be loose?

2)in mdi I ask it to move .100" and the motors do not move nearly as
much as a .100" step in manual mode. It seems I have overlooked a
variable somewhere.

If you have any ideas let me know.
Matthew