The question is, however, why did this suddenly start happening after several weeks of perfect operation, during which I've been streaming data off the board? We have several more boards on order. Will this be a recurrent problem, or does it only happen with some hardware?
I really think the root problem is somewhere in either your Putty application or in your PC USB driver, or something else software related in the PC. I use a serial terminal program a lot (Brey terminal) and often leave it opened on the desktop as well as having the arduino IDE open. The IDE is well behaved in that after a upload it releases the comm port automatically. Brey terminal has a connect/disconnect button that also allows releasing of the comm port manualy. So I have no problem going back and forth between uploading sketches and monitoring the serial data on brey terminal, as long as I remember to hit the disconnect button on brey terminal before trying to upload from the arduino IDE. I have never had to unplug the arduino board from the USB.
I use windows XP SP3 and a wide variety of arduino boards.
Lefty