I also appologize for the delay. For some reason I didn't get a notification of your reply, which is why I didn't answer right away.
It sounds like auto-zero mode works, which is a good indication that the error is
being introduced inside the SCXI-1125. This means that the module's
offset errors have either drifted outside of the specifications, or
that the module was improperly calibrated at some point. If you don't
already have it, you can download and install NI-DAQmx 8.0 or later,
which will allow you to perform a self-calibration of the SCXI-1125,
which will reduce the offset errors of the module.
http://digital.ni.com/softlib.nsf/websearch/D31D46FFFB745ECA862571490053EAB8?opendocument&node=132060_US
To perform a self calibration, perform these steps:
1) In MAX, find the DAQ device that is connected to the SCXI-1125. Right click on the Device and select "Self-Calibrate".
2) In MAX, find the SCXI-1125 module, and also Right click on it and select "Self-Calibrate".
Now, perform your same tests to see if anything has changed.
If you still have an offset error, then like Sacha said you should definitly try inputing a true voltage source, like a battery, to make sure that the inputs are being scaled properly by the calibration data stored on the SCXI-1125s. If you still see large errors or incorrect readings, then you should probably return the module for repair.
Finally, if Auto-Zero is working, you probably just need to ensure that you are using it properly. The easiest way to enable auto-zero mode is when you create a Task in MAX, you simply go to the Device tab of the task and set Auto-Zero mode to "Once". Then, when you save this task, you can use it in LabVIEW.
I hope this helps.
Regards,
Logan Kunitz