Maybe you have accidentally set it to highlight on search, rather than filter?
A lot of people seem to have been confused about this, so in the latest update, that setting was moved over to Preferences ==> Searching, uncheck "highlight search results instead of restricting the book list to the results"
Before calibre 1.11 this button would toggle it on and off:
EDIT: On Windows the setting will say this: "Show a quick toggle button to switch between highlighting and restricting results next to the searchbar"