Hi Alvaro - The freezing happens with both mega or duamilanove boards. I'm glad to hear it is not related to Mac or Java but only arduino sketch because i really hope success with arduino scope for many of us wether PC, Linux, Mac,...
To answer your query and after many trials yesterday & this morning: it freezes after a while without intervention on my side and as I mentionned to you privately, there is no packet loss detected by software when I lauch Mac terminal shell. To lauch again the scope, I usually press one time, sometimes two times the dual channel button with my mouse so it works again then freezes after a while but the working duration is random (can be a few seconds, sometimes one minute).
Hope it helps