I really think there is a problem in the firmware.
I modified your firmare removing everything but the analog readouts and sending a byte (128 + pin number) before every readout to see which analog I'm reading, I also modified arduino-help.pd and arduino.pd accordingly and now it works ok.
you can download the modified firmware and patches here: http://www.davidemorelli.it/public/Pduino-modified.zip
...am I the only one having problems with multiple analog inputs? have you tested it with multiple analog ins?
This sounds a lot like float voltages. The Arduino's/Atmel's analog inputs are very sensitive to voltage. So if you don't have analog pin tied to either ground or 5V (e.g. via a resistor), then there will be tiny voltages on those pins, which the Arduino will dutifully measure and report. Try grounding any open pins.
yes, i did it on the last unused pin, maybe I get strange values because I'm using quite long wires but the fact that I can read the first 3 analog but not the last 3 is suspicious.
best, davide.