I have had this issue before:
To fix it please start a remote desktop or connect a display + keyboard + mouse to the robot, then minimize to the desktop and follow these steps:
1) Open a standard cmd window
2) Type puttytel -vio, this will open PuttyTel, click YES if a dialog appears
3) Enter the command SRThinMMAdmin_setPositionReference x,0 in PuttyTel and confirm with Enter. Observe upper/lower case (x is the axis index - 0 stands for axis 1 and 6 stands for axis 7)
4) Move the affected axis to its mechanical zero position
5) If the axis has independently mastered itself, it must first be unmastered
6) Then master the axis
Hope this helps