I did exactly as you said and everything seem to be working just fine. I fixed the axis to be normal, and calibrated the direct ones, followed the [Joy Letters] documentation and set AutoAssignLetters=Yes, removed joystick 7 as it was a duplicate, and everything seem to be working just fine now. I restarted a couple of times and tested the engine start procedure a couple of times and no unwanted flap extensions.
Greatly appreciated John.
Cheers,
Mustafa
p.s.: I ended up not needing the JoyId software, nevertheless I couldn't download it even if I wanted to as the airgroup51.net link for it from Pete's post requires you to be logged in to download the attachment, and airgroup51.net are not accepting new registrations.