I knew it would be something obvious. I installed uisp from the Ubuntu tree (version 20050207-3) and symlinked uisp from the /usr/bin to the tools directory and it works perfectly. I haven't tried doing much so far (such as serial communication with Processing), I just hope I won't have any "64 bits" surprises such as the librxtxSerial.o
At last, I would switch to a 32-bit version of Ubuntu.
If I can get it running smoothly under linux, it's even better! In fact, I will be teaching Arduino in two weeks (that's why I may sound so stressed about getting it running) and if I can restrict the work on linux, it will be a reason for my students to discover it.
Under Windows, I'll check later (as I'm running unix right now
) but I remember setting the JAVA_HOME to the right directory. I'll double check the backslashes but, except from the PATH environment variable, I'm pretty sure I changed all the others.