I can't give you the gory details but I think it involves the method that is used to reset the arduino board connected to the comm port. In older versions of the IDE the IDE did the toggling of the DTR comm control signal which then resets the board, and then the IDE passed on to AVRDUDE to actually perform the upload. In newer versions of AVRDUDE and the IDE, the IDE does not issue the DTR, but rather AVRDUDE handles it.
So my guess is you need a newer version of AVRDUDE, or a properly setup avrdude config file and or the new avrdude option command to handle the dtr action.
Something like that.