User blog comment:Dopp/Technical Update: May 15, 2012/@comment-4507874-20120517060032/@comment-2026043-20120517143512

Set the width of the .WikiaSearch input[type="text"] element to 220px, in the MediaWiki:wikia.css stylesheet, like this

.WikiaSearch input[type="text"] { width: 220px; }

It should fix this issue, maybe permanently, maybe until Wikia roll out their own fix.