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.