I am using emacs26.3 with the major mode "Javascript-IDE" activated. When I type M-x comment-line the desired effects happen in the editor. However, when I type the shortcut C-x C-; I have this output:
Comment column set to 2
And the line is not commented/uncommented. C-h b shows that is the key binding is correct.
Here is my emacs configuration: https://github.com/Amine27/dotfiles/blob/master/emacs.el
Are you using emacs in a terminal? A terminal cannot transmit all combinations of keys and modifiers you could press. I can reproduce this behavior when I run emacs in my terminal (pressing C-; just produces an ordinary ;), but when run in my OS's windowing system emacs registers the C-; chord as desired.