Hi all,
After some research, trial and error and some circuit corrections (I have to admit I did some mistakes there and thought it was in the code), I finally managed to get two multiplexers - one with potentiometers and one with push buttons - work correctly and gather the data in Pd in the right order.
You have to wire you pots as shown here http://bildr.org/2011/02/cd74hc4067-arduino/
but I used a bit of a different code (attached). The push buttons are wired in a similar fashion, but the way you wire a push button.
So this way you can really have lots of analog and digital sensors, knobs, sliders, whateveryoucallit with just one arduino and some multiplexers! You can build your custom made controller for little money...
http://www.pdpatchrepo.info/hurleur/my_mux2_analog_digital5.ino