The non-standard layout of the forum (some replies, with the latest date, are supposed to, or not supposed to? go right in the middle of the page rather than to the end of the full convo) may not work out for all kinds of, otherwise normal forum interactions. Here's an example: https://portableapps.com/comment/235768#comment-235768
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The reason for the difference in nesting is the reply button the commenter has clicked.
Clicking the "reply" button in a comment will nest the reply under that comment, but clicking the column-width "Post reply" button at the bottom of the thread (which many users do) adds it to the end of the thread (because you are replying to the original post with that button, not any individual comment).