It appears there is a problem with directly replying to a comment, i.e. if you left click on reply, it doesn’t thread it under the comment you are replying too.

I have no idea why. We recently upgraded to a newer version of WP and it may be a bug in that.

However, there is a workaround that Billy Hollis noted in the comment section of one of the posts. If you will left click right click [edited by Billy] on “Reply” and open a new tab, the reply you leave will be threaded with the comment.

Sorry for the inconvenience, but we do have a work around until we figure it out.