Hi Mike,
Well the manufacturer of the tool will tell you this tool is not designed for production.
What probably happened is you had a problem during the init with a signal having some noise or something of the same spirit. As the erasing sequence was not performed properly, the MCU could not be re-programmed.
I often have trouble with this tool. The MCU seems just dead. I go for a coffee, come back and it works fine... Maybe something floating in my EVB which keep a level thanks to PCB capacitance.
Moral of the story: go and take a coffee... Or as a computer user: "HAve you tried to switch it off and on again ?" (British will understand)
Cheers,
Alban.