Favicon
Use $wgFavicon to tell MediaWiki where the image is located.
I have a similar issue. My windows server is hosting several sites so the favicon for the wiki needs to be in a folder for that site... however when I use the php $wgFavicon settings in the localsettings.php file nothing happens.
What is the content of $wgFavicon?
wiki.hotdocs.com
It shows up for me. And I see <link rel="shortcut icon" href="/favicon.ico" /> in the head as expected.
However, the favicon is actually a PNG and Internet Explorer only supports ICO favicons. If you're using Internet Explorer you won't see it.
what browser are you using? where does the favicon say that it is a png?
I just looked with firefox, safai, and chrome, and like you said they all work. But there is still the issue of why would IE think the
<link rel="shortcut icon" href="/favicon.ico" />
is a PNG?