I find the behavior incomprehensible. This had been working, then suddenly we can no longer communicate to the board.
Note the oddity. It is able to read from the device, so this is not that someone else has the serial port in use. One suggestion on StackOverflow was to (re-)install the '340/'341 driver, which we did, and nothing changed. It is not an access denied on open; it has clearly opened it. We have the same problem whether we have the chip installed in the breadboard or not (thinking we might have a problem with the circuitry it is interfacing to). If we just bring up the serial monitor and hit reset, we get the end-of-setup message coming out, so we know the chip is working. It's just that the program in it is not quite right and we can't get another program to load. Very frustrating. Particularly because I am trying to get this working over Skype, so I can't actually see what is happening.