Toggling comments does not work when using custom languages which are derived from standard languages.
I’m using the Seti_UI theme which adds icons for some specific files, e.g. Gruntfile.js which has a different icon than normal JavaScript files. This way you can find relevant files more quickly.
In Seti_Ui there are the .tmLanguage and .tmPreferences files:
You can see that the file type extends source.js.
When opening a Gruntfile.js the syntax highlighting is set to Gulpfile JS, not JavaScript. Commenting lines using the toggle_comment command does not work in this case.
After setting the syntax highlighting to JavaScript, everything works fine.