If the watch dog timer is enabled at the beginning but it is then not strobed periodically to keep it reset it will then timeout and make a reset of the processor. For this wo work correctly the programming code itself must support strobing the WDT. When the host end of the download protocol gives the state change that programming mode is done it exits from the mode to some code that does not support the WDT...and then shortly thereafter....RESET time.
Michael Karas