Or just recent activity. I think I've seen it happen to accounts that were digging in their heels and vigorously defending some wrong/incorrect/unpopular point they made upthread. Then all the sudden they're mentioning the post limit and editing posts to reply. I'm guessing it's a combination of high (recent) post volume and down-votes that triggers it.
It's part of the philosophy of HN. Arguments that are just people repeating the same points back and forth aren't interesting or enlightening.
I get the rationale for it. My only gripe with it is that it says "you're posting too fast, wait a few minutes" when I wasn't posting fast, and it blocks account activity for hours. I don't like automated messages that lie.
I think there are two things at play here. One is when you're rate limited because dang limited you because you're violating the site guidelines. It's a less drastic step than all your posts showing up as dead.
Second is, the further you are "to the right" in a discussion - the more parents you have to go through to get to a top-level comment - I thing you eventually get to a delay there, just to stop threads from marching off to infinity with two people (who absolutely will not stop and will not agree, or even agree to disagree) going on forever. I'm not sure what the indent level is that triggers this, but I would expect some sort of exponential backoff.