I found this quite old thread, but the solution here is the one and only that seems to work for me.
I had also the problem that Windows changes the resolution if the AVR switches input or goes to standby.
Many other solutions did not work (like block Pin 19 on HDMI connection) or produced other problems.
Because I already use Eventghost to map key bindings between Kodi and PowerDVD it was easy to setup the solution here.
(Also I switch Denon / Marantz AVR on and to the correct input with the help of Eventghost and a network connection to the AVR,
so the AVR is in standby at Windows Boot. )
I had only setup a second Window/fullscreen toggle command in eventghost event, otherwise kodi only switches in window mode.
I'm not sure why, may be because I've a delay at windows start for the kodi autostart to be sure Windows has build up the network connection my NAS....
Many thanks at the OP and all that helped to create this solution.
P.S. For all with the same problem: I'm using this with Windows 8.1 with Kodi 16, and I think it should also work with Windows 10