Thread:Project:Support desk/Logo only works in Vector Skin/reply (3)

That configuration looks good. Maybe you should put the image into images/ directly, so that you get it with $wgLogo = "$wgLogoPath/Wiki.png";, but apart from that it should work.

The thing is that some skins (like Vector) use the logo, while others don't. Modern is among those, which do not use the logo. You can also check that with Wikipedia: Call a page and append useskin=modern to the URL and you will see that also on Wikipedia the pages will come up without logo. So this is neither a bug nor a configuration problem on your site; it is just intended that way.