Stuck at "Entering bootloader mode"

I have Arduino Leonardo flashed with ArduinoISP sketch which I'm using for years now on my Linux desktop with avrdude without issues. I've tried your avrdude build for Windows with the following command:

avrdude.exe -p atmega2560 -P COM12 -b 19200 -c avrisp -C avrdude.conf -e -V -u -U lock:w:255:m -U efuse:w:252:m -U hfuse:w:208:m -U lfuse:w:255:m -vvv

It's stuck at "Entering bootloader mode...". Here's the full output:

avrdude.exe: Version 6.3.1.1-windows
             Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
             Copyright (c) 2007-2014 Joerg Wunsch

             System wide configuration file is "avrdude.conf"

             Using Port                    : COM12
             Using Programmer              : avrisp
             Overriding Baud Rate          : 19200
avrdude.exe: Found device at port 'COM12'
avrdude.exe: - InstanceId: USB\VID_2341&PID_8036&MI_00\6&24E919D7&0&0000
avrdude.exe: - Port: COM12
avrdude.exe: - Location: Port_#0001.Hub_#0001
avrdude.exe: - ProductName: Arduino Leonardo
avrdude.exe: - IsPresent: true
avrdude.exe: - IsCompositeDevice: true
avrdude.exe: Entering bootloader mode...

I suspect this might have something to do VID/PID detection - my guess would be that Leonardo is detected by that combination and avrdude tries to send it to bootloader. However, it's not Leonardo that I'm flashing, it's custom mega2560 board... I could be wrong though.

mariusgreuel / avrdude

Stuck at "Entering bootloader mode" #5