My wild guess:
A high value resistor will appear to be a high impeadence source to the input of the DAQ device. If the interchannel sample time is small compared to the RC time constant of the resistor and input capacitance of the DAQ device (Check spec here) there will not be enough time to full change the input cap to the new voltage while scanning.
THis is characterized by
1) Both voltage look right when measured by themselves.
2) One voltage seems to follow the other.
3) THe problem is less severe when sampling at slower rates.
Done guessing!
Post some code for us to look at! WE do better with pictures.
Ben