FreeBSD 9.x has file-5.23 that introduced terrible performance regression fixed with file-5.25 which was imported and MFC'd to 10.x but not to stable/9. For the reference: http://bugs.gw.com/view.php?id=474 Please perform MFC r287453,287454,288143 to stable/9 too.
Over to current maintainer of file(1) and committer of SVN revisions in question.