It only appears for me next to the post when I click "link" and view a comment individually. I assume this is to prevent knee-jerk flagging. Not sure what the karma limit is.

For me I noticed the flag button for the first time when I reached around 150 karma points.

I can flag posts but not comments, and I'm at 118.

I do notice, however, that I see the flag link for your comment now that I've hit the reply button. I think this is a bug.