I upgraded libinput in Debian unstable and my custom trackball Options are now being ignored. I filed a detailed bug report at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823214 with reportbug, which includes system and logging information, including exact version numbers. They said I should file this information with you, please let me know what information you need above and beyond the debian bugreport (or if you want me to copy/paste parts of that report here)
as said in the debian bugreport, the InvertX/InvertY options aren't supported in libinput and thus not exposed by the xorg libinput driver. For now, you'll have to use a custom xorg.conf snippet that sorts higher than the libinput config snippet to manually assign the evdev driver.
fwiw, the libinput commit below adds rotation for trackballs to libinput. commit d1a8a92184684474bff9d4c29a67da416d40fb26 Author: Peter Hutterer <peter.hutterer@who-t.net> Date: Tue May 3 13:52:53 2016 +1000 Add support for relative device rotation (trackball only)
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