While working on moderately to large sized C++ projects, I have also noticed that the comment toggle ( ⌘ / ) intermitently stops working, even when all the key bindings are enabled, and the function is not greyed-out in the Editor → Structure → Commnent Selection.
I realized that it only happens for specific source files. If you have multiline /* ... */ comments, it is possible that they overlap, are nested, or not properly closed. This probably confuses the parser that the editor is using. The problem is resolved by deleting the messy, commented-out code. Running a Build Clean also seems to help.
I'm not sure if this is the same problem being discussed here, but I thought I might add my experience.