Query about noise levels and input terminal configuration when recording analogue voltage input

[xenomorph99]

I am using a PXIe 6363 connected to a BNC2090a to measure voltage output from a patch clamp amplifier. The output signal source of this amplifier has a signal ground that is isolated from the chassis and mains ground via a 100 ohm resistor. I have plugged this voltage input to one analogue input channel (AI0), and the signal ground to the paired analogue input channel (AI8). I am confused as to a particular phenomenon I have regarding noise.

If I set the BNC2090a switch to RSE, but set the analogue input terminal configuration to differential, I get a great signal to noise level. I know that these two settings are supposed to match.

However, If I set the BNC2090a switch for the channel to differential, my noise drastically increases. Also, if I change the analogue input terminal configuration to RSE, my noise drastically increases.

Can anyone explain why this might happen? And if what I did to achieve low noise will cause problems?

[Ben]

You may be seeing what the spec called "CMR - Common Mode Rejection" that describes the extent to which the differences in ground potentials can vary and still get a good reading.

When you "accidently got it right" the grounds got tied together.

Just wild guessing on my part so if I am wrong you can get your money back.

Ben