Simplified problem : A 1 V battery and 4 V battery are read in differential. Starting from a sampling rate of 20000 the 4 V signal increases the 1 V signal. Real problem : force sensor signal influenced by encoder digital signal (0,3 and 4 V) : offset more than 2 V on force sensor signal
The batteries are floating signals; thus, when you read them in differential mode, you must use bias resistors (about 47 kiloohms) in order to discharge the bias currents. Otherwise, you might see unaccurate readings. I have seen this problem before, and maybe this is what it is causing to get bad readgins. By the way, the bias resistors should be connected from the negative lead of signal to the AIGND of the NI board. Finally, see if the force sensor signal and the encoder digital signal are floating or grounded.If they are also floating, that might be the issue.
The best way to go about that is to specify a interchannel delay, long enough so the Instrumentation Amplifier have time to settle properly.
If you don't specify the interchannel delay, NI-DAQ driver will do it for you, but, it will pick the lowest value possible with your hardware type, and sometimes, depending on the input signals you might have, that selection creates a cross talk in between channels.