Few things to note.
If I recall correctly, the magnitude of the nonlinearity is proportional to the total difference in potential across the current sense amplifier inputs - in other words, different currents at 2V produce different errors.
The error is caused by the common-mode voltage, so one channel held at a fixed voltage and used as a virtual ground (at 0v, 2.5v, 5v, etc) will not show this error and will accurately measure the full scale current.
We'll be starting a beta distribution of new SMU hardware in the not too distant future, which resolves the 2v common mode error issue and offers greater precision. Details will be posted to this list in the next few weeks.