Over at http://www.sciencebasedmedicine.org/ we're using Jetpack for commenting. We have "Comment author must have a previously approved comment" checked, and "An administrator must always approve the comment" unchecked but all users are having their comments require moderation no matter their previous amount of approved comments.
The number of links required for automatic moderation is set to 3 and this is happening with comments with even zero links.
I've done some searching here and via Google and one solution was to clear the word lists for moderation and spam to see if that helps. We've tried that and it hasn't helped at all.
I've also tried simply toggling the settings on/off (because you never know) and that didn't work either.
Commenting is very active on this site, but we've also got a problem with sock puppets and fake posters that requires some fairly stringent moderation.