Its posssible the axis is binding at some point.
Also you might want to check the wiring on that axis, even if it looks good a high resitance connection could cause the problem.
The signal & wiiring coming from the BOB or computor for that axis would be something else to test.
Noise getting in to the system that is only close to the X axis wiring. If your running a VFD this is very possible.
You have changed motors, and driver board so it should be in one of the area's I meantioned. A scope would be good to help pinpoint the problem.
Jess
GOD Bless, and prayers for all.