Have you got decoupling on the multiplexer chips?
http://www.thebox.myzen.co.uk/Tutorial/De-coupling.html
Are you suffering from cross talk, that is one channel affecting the other?
To test:-
Start off with only one channel connected, connect it also through another chip analogue input look at the readings are they similar.
Then add more channels but don't look at them in the software. Do they now behave differently?