I’ve run into an issue where Ctrl-/ shows as activating the editor:toggle-line-comments functionality, but nothing actually happens in the file. Rebinding this (to e.g. ctrl-i) doesn’t change the behavior, and running atom in --safe mode also behaves identically.
This was working for me around Nov/Dec last I recall. I use a Logitech G710+ keyboard with a US language setting and haven’t had an issue like this before in atom.