Faster method:

• Visit the wiki (eg, on this install it's https://secure.phabricator.com/w/)
• Change the dropdown next to the search bar to "Search Current Application"

• Perform a search using the search bar at the top of the page

You only have to perform the second step once (it's sticky), so this makes searching the wiki a two-step process. It does not, however, fix your custom search engine use case.

By inspecting the network call that that search field makes, I was able to find a URL for the custom search engine use case:
https://secure.phabricator.com/search/?query=foo&search:scope=application&search:application=PhabricatorPhrictionApplication&search:primary=true

It looks like your install is running custom CSS (the icon is there, just white)

(ps there is a "light" theme in Phabricator now, if you want to use it properly)

Our install isn't running any custom CSS. One of our engineers published a Chrome extension that re-skins Phabricator, and it looks like @ianm is running that extension. Ian, disabling the extension should help.

(I'll also follow-up with the engineer responsible for that extension.)

See T4213 for "we change CSS all the time and your stuff will break every few months if you mess with it".