maybe the motor is not configured properly, try the following:
put your 4th axis scale at zero.
goto settings screen (alt-6) and press the set steps per unit button (bottom left of the screen)
then select the A axis and tell the wizard to move 100 units
using the scale in the 4th axis read how far it moved and enter this value
accept the change
Now move the axis any desired amount and verify if its correct. After a couple of iterations of this procedure you should have a pretty accurate 4th axis, no need to do it more times because you will start jumping between two similar values each time.