Thank you for taking the time to report a potentially serious problem.
AVG free-version isolated an unidentified nuisance-category virus in AVRDUDE on my system.
“An unidentified nuisance-category virus”? What is that?
It was only in the 1.52 download however.
Which is the exact same AVRDUDE that was included with Arduino 1.0.2, Arduino 1.0.1, and Arduino 1.0. (The Arduino 1.0.3 version is a different size.)
If your copy of AVRDUDE is not identical to the previous versions (except 1.0.3) then there is something else on your computer infecting executable programs.
This, and my never-used COM3 modem was activated recently, screwing with everything conflicting with Arduino-USB.
Are you claiming ARVDUDE accessed COM3 without being told to access COM3?
What size is the AVRDUDE.EXE file(s) on your computer?