Hello Kevin,
What configuration mode is your device using (differential or referenced-single ended (RSE))? Since the power supply is a grounded source, you will want to make sure you are not using RSE mode because you will be tying the ground of the PCI-6031E and the ground of your supply together. This could cause ground loops and induce offsets and noise.
When connecting your signals in differential mode, you will connect the signals between CH X and CH X+8. For your battery, which is a floating source, you will also want to use bias resistors (connect a resistor between CH X+8 and AIGND). Chapter 4 of the user manual (linked below) goes over connection considerations for the different configuration settings.
PCI E Series User Manual
http://digital.ni.
com/manuals.nsf/webAdvsearch/06F1C9FB0D0BA5C286256C010057461B?OpenDocument&vid=niwc&node=132100_US
Are you seeing this when reading from both channels simultaneously? If yes, another possibility would be cross-talk. This is when one signal shows up on another signal. This is usually caused by a source with a high-input impedance. I would measure the input impedance of your signals and make sure that they are not over 1 khom. You can reduce the input impedance of a source by using a non-inverting op-amp circuit. The documents linked below go over cross-talk and how to eliminate the effects of this phenomenon.
Data Acquisition: Troubleshooting Unexpected Voltages or Cross-talk in Analog Input Channels
http://digital.ni.com/public.nsf/websearch/B9BCDFD960C06B9186256A37007490CD?OpenDocument
How Do I Create a Buffer to Decrease the Source Impedance of My Analog Input Signal?
http://digital.ni.com/public.nsf/websearch/CF83426BC3AC514A86256C10005A4771?OpenDocument
Using a
Unity Gain Buffer (Voltage Follower) with a DAQ Device
http://zone.ni.com/devzone/conceptd.nsf/webmain/CD57A73721E0612586256BAE0055CDD9?opendocument
I hope this helps.
Regards,
Todd D.
NI Applications Engineer