AVRdude + Arduino leonardo: can't flash over bootloader, not in sync: resp=0x3f
You're specifying the wrong bootloader protocol via -carduino. The Arduino bootloader is for boards using the Diecimila bootloader. The Leonardo uses the "AVR109" bootloader - named after the Atmel Application Note which describes its protocol.

Try this command on for size:

avrdude -cavr109 -P COM5 -n -p m32u4 -b57600 -v


Don't forget to press the reset button (or open and close COM5 at 1200 baud) first to run the bootloader.