Hi all,
I have the same problem with my Arduino Uno / Ubuntu 10.04 LTS/64 bit (I can break the look with Win7, however).
Would it be a solution to add a switch to the setup and within the serial look check whether the switch is pressed. If the switch is pressed the serial loop is exited. This would be a software/cheap hardware solution to stop continuous data stream to the serial port. Then it should be possible to send another sketch to the Arduino.
Cheers
Karl-Heinz
PS: I am not a programmer, but an endless loop without any control does not look like good programming practice to me.