I solved the problem of working with protege under windowsXP by setting the COM1port settings to:
bits per second: 9600 (default)
data bits: 8 (default)
parity: none (default)
stop bits: 1 (default)
FLOW CONTROL: Xon /Xoff (none = default)

These settings can be found in:
Start -> Settings -> Control Panel: open "System"
then go to: Hardware - Device Manager;
dblclick "Ports"
right-click "Communications Port (COM1)" and select "properties" and go to "portsettings" and fill in the above settings.

Good Luck !!!