Spybot doesn't scan automatically every day. You'd have to run it yourself. There is usually an automatic scan scheduled for the first of every month, though.
However, as per your post title, the file scans aren't automatic at all. And I thought I'd let you know in case you are new to Spybot that the file scan let's you scan the files you select, and is not the full spybot scan. The full spybot scan is called the System Scan.
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