Just fyi, I've never been able to rate article comments. I can rate articles themselves though.
I just get "There was a problem storing your reputation vote."
The exact same problem occurs with journals. I can upvote journal posts, but not journal comments. Same error message also.
I've just been ignoring it - it's not hindering usage of the site and thus is really low priority - but I suddenly realized I never submitted a bug report so you gents might not even be aware of the issue.