Hi Federico,
I have played again with my demo sketch and I figured out that the hangs only occur if serial data is received!
I have connected the XBee shield to the Yun via the digital pins 8 (RX) and 9 (TX) and it takes only a few minutes when the first hangs occur. Then, I have disconnected pin 8 (RX) and everything worked fine. I kept the sketch running for an hour and everything was stable.
So, it has definitely to do with the serial data. I have 5 XBee nodes which send a IO sample every minute to the XBee coordinator which is connected to the Yun.
Could you simulate this load with a Arduino UNO which generates some test data and which you connect to the pins 8 and 9 of the Yun?
Could it be that the hangs have something to do with the interrupt which is used by the SoftwareSerial?
@Fred: It seems that you have another network related problem.
Bye,
Sebastian