This regression was apparently introduced in Emacs 25. It is still present in the 26.1 pretest. See the attached screenshots, both from `emacs -Q', one from Emacs 24.5, the other from Emacs 25.3.1. 1. The #...# files are missing. 2. The .* (dot) files are missing. 3. The order of the other files is changed. I see the same problem for the default switches: -al. I find nothing in NEWS about such a change. And I find it hard to believe this would be by design and not an accidental regression. On the other hand, it's also hard to imagine that no one else has reported this. (But perhaps this is a duplicate?) In GNU Emacs 25.3.1 (x86_64-w64-mingw32) of 2017-09-26 built on LAPHROAIG Windowing system distributor 'Microsoft Corp.', version 6.1.7601 Configured using: 'configure --without-dbus --without-compress-install 'CFLAGS=-O2 -static -g3' PKG_CONFIG_PATH=/mingw64/lib/pkgconfig'