A few months late, but it's doing what it's being told to do. Checked Out By User returns documents that are currently checked out by the specified user, and turning off the flag to show checked out files disables any filters related to checked out files. To find files that have previously checked out by a specific user, use the Version Created By User variable. This will return all files where the specified user was the most recent person to check in that file. If you want to dig a bit deeper and get all the files that they've ever worked on you'll want to also use Search Previous Versions.