I go to this story
and read the comments for a while. Then I decide I want to change the threshold to -1. After this, I notice that certain comments are gone. Searching for "science nazi" in Firefox turns up two posts on the first page; but after changing the threshold, neither post can I find, even though I page through all six pages. The same result occurs when searching for "deadgoon" (one of the posters; actually it's "deadgoon42"). (I didn't take the time to search for the other poster, yfkar.)
Maybe this will even correct itself by the time I post this, but I wonder what is going on here.