Unfortunately, that reply can sometimes be days, weeks or who knows how old, and HN doesn't inform you of replies to your comments, so unless you happen to see it when it happens you're stuck with having to intuit that "you're replying too fast" is an extremely passive aggressive flag on your account and not just a general site-wide rate limiter. Or notice that your flags no longer work, or your vouches no longer work, or any number of even more subtle effects.