Beam,
You can programmatically perform a self-calibration. In LabVIEW, you can call the E-Series Calibrate VI within the Data Acquisition>>Calibration and Configuration subpalette. If using a text-based ADE, you can call the Calibrate_E_Series NI-DAQ function.
You are right in that the PCI-6036E device should be supported by the online diagnostic utility; that should work. Make sure you have NI-DAQ 6.9 or higher and Internet Explorer 5.0 or higher.
Also, is the voltage you are reading floating or ground-referenced? If the source is floating then you should use bias resistors when configured in NRSE or differential mode. Chapter 4 of the E Series User Manual (linked below) goes over how/when to connect bias resistors. I would take a look at this chapte
r and use it as a reference for connecting signals. I hope this helps.
PCI E Series User Manual
http://digital.ni.com/manuals.nsf/webAdvsearch/06F1C9FB0D0BA5C286256C010057461B?OpenDocument&vid=niwc&node=132100_US
Regards,
Todd D.
NI Applications Engineer