Wihout a schematic about all I can say is to trouble shoot it with a multimeter. With the multiplexer connected to the arduino, ensure a pot connected to the multipler point that isn't working is inputting ~+5v to the multiplexer. Then check the voltage at the control points on the multiplexer being supplied with +5v from the arduino to see if the points are actually being supplied. Then check the point where the multiplexer output connects to the arduino to see if there is the ~+5v on the point. Ensure all the chips and the arduino have a common ground.