It sounds like the torque limit settings for that axis were somehow modified. In Measurement and Automation Explorer (MAX), look at Control Loop Settings for your axes. Select the Torque Settings tab at the bottom of the window. This page has the torque limits which, by default, are defined in terms of a voltage range. These values may have been altered at some point, causing your axes to have different ranges.
In the future, you could try using the Load Torque Limit.flx function to specify the primary and secondary output limits for that axis.
Let me know if you have any additional questions on this issue.