Stories with lots of comments are rank-penalized. "Whiteboard coding is bad" submissions attract a lot of "me too" comments and quickly fall off the first page.

It seems counterintuitive for a forum to want to penalize threads that actually get traction.

I think part of the problem is that everyone that comments then upvotes. Same as askreddit, for instance. Plus I wouldn't be surprised if these are manually pushed out of the top, there's like one a week and the mods must be getting sick of it

It seems to me that they may be trying too hard to intuit the quality of a thread based on behaviors which don't explicitly indicate it. I think that the only behaviors that should push a thread down are downvotes and flags, not upvoting and/or commenting in the wrong order, or only doing one but not the other.

You can't downvote a submission.

Moderately sure that comment threads on a submission are strictly ordered by score.

You can indirectly downvote a submission by downvoting the comments, or (apparently) by not upvoting them.

OTOH, I have definitely noticed that stories with a high upvote/comment ratio seem to have better quality. In the absence of story downvotes, it makes a certain amount of sense to regard a comment without an upvote as a weak signal that the story is low quality. Penalizing stories with lots of comments relative to votes makes sense to me. (I don't know if that's what actually happens, just saying it wouldn't surprise me)

That would be my bet too. I would say comment/minute, not just absolute number of comments.