Comment threading goes haywire when posts are deleted

I posted this in Miscellaneous earlier, but it’s gotten no responses so I thought I would try here. Apologies for the double post.

Here’s what I can figure out: if I delete a comment (for being spam, or a duplicate post or something), the comment nesting/threading after that post goes all crazy and comments don’t nest/thread properly.

Here’s an example:

https://www.yousuckatcraigslist.com/?p=5076#comment-57051

I’ve linked to a comment that was a reply to a spam comment that I deleted. If you scroll further down the page you’ll see that there are very few nested/threaded comments (although there are some) and there’s lots of comments by people saying that their comment didn’t end up where it was supposed to. [If you scroll UP the page you’ll see that nesting/threading was working just fine until the point where a spammer posted.]

Is this a WordPress issue, or is this an issue with my theme? Comment nesting/threading works fine as long as I don’t delete posts, but the minute I do things go all wonky.

I’d appreciate any help anyone can offer. Thanks!