Be sure you short out all your unused channel inputs. The multiplexer Will show crosstalk if you fail to do this. You can set the software trigger of a selected channel to maintain synchronization. Preferably the square wave channel.
Also, check the obvious, like your DAQ configuration...is it differential, single ended, etc.
Hope this helps!
Chutla
Eric P. Nichols
P.O. Box 56235
North Pole, AK 99705