Have you done an independent check of directory contents before and after a given run? E.g. if it runs at 09:00, you should do a (gnu) "find" (or something equivalent) on the target directory a couple minutes before execution, and again a minute or so after execution.

It may be that having %Dir tied with IO::Dir, while trying to modify the contents of the target directory, is causing unexpected side-effects (or failure to behave in the expected manner), and the problem is not with the @FileList array, but rather with the directory contents.