Hi PRJ-
I have been testing with my PCI-6040E E Series card and haven't been able to replicate the behavior you are seeing. Are you sure that all of your connections are correctly made for RSE? You need to keep in mind that differential connections are fundamentally different from RSE. I would suggest that you verify for RSE that you are connecting your signal (+) to the numbered input channel and signal (-) to AIGND. For differential you should connect to the input channel (X) and (X+8) for signal (+) and (-), respectively.
I would also check to make sure that you are not seeing ground loops in your systems as this can sometimes introduce skew into RSE readings.
In general, differential measurements are advised because of their ability to provide better common-mode rejection and to remove the possibilities of ground loops. NRSE mode is another alternative that can be used if sacrificing two input channels for a single measurement is not a good option.
Hopefully this helps-
Tom W
National Instruments