From Non-Mux version:
Serial.print("DATA, TIME");
Serial.print(",");
Serial.println((int)(Voltage*100));
From Mux Version:
Serial.print("DATA, TIME");
Serial.print(",");
Serial.print(digitalWrite(pin1, HIGH));
Serial.print(",");
Serial.println(digitalWrite(pin2, HIGH));
I don't see a adc conversion in the mux version nor do I see it trying to be printed.
What is the mux version trying to print? The result of the digitalWrite function call?
P.S. You forgot the code tags when you posted your sketch.
P.P.S. This isn't a PLX-DAQ problem, it should not be part of this thread.