Small Update, I also had troubles with the bootloader of the standard Mega R3.
It crashed because of watchdog not working correct with the default bootloader.
Flash you mega with this link, download the HEX and your code with watchdog will work without buggy hangs that only will continue after power unplugging.
http://code.google.com/p/arduino/issues/detail?id=181&can=1&q=watch