Setting the favicon in the ACP doesn't permit to see it in the ACP pages, it will be only displayed on public pages, to see it within ACP pages you have to upload it manually in the root directory.
My forum wont read from the root...lol
/portal/community/Xenforo files (I am assuming this is the root)
the root had the favicon for the custom index page I use... an intro-video.
Otherwise the video redirects to Xenforo
When I tried to put the fav icons into the community folder (which I think is the root you guys are talking about) nothing changes. So... have to investigate this further I think.