That's really weird. Are you sure you're using the right serial port (com port)?
The export button simply recompiles your code and runs uisp, a program to upload the code to the board. I don't know why either would make your machine reboot. What's in the file called "stdout.txt" in your Arduino application directory?
Are you running any other programs that use the serial ports, com ports, or USB ports (like a PDA sync application or a vigorous virus checker)?
Have you installed cygwin on your machine?