Thanks I agree, I know about the 1200 baud reset to bootloader port.
Pressing the reset button does the same thing, the board comes up correctly on the bootloader port.
The problems are when avrdude runs so you might well be right but that is undocumented??
I also tried the 1200 baud reset via software and that shows the same issue as the command line.
Either way it should be possible to upload via hard reset/bootloader.
ps: and yes the Leonardo works as expected in all cases.