Replies in thread showing out of order

I don’t understand it either, I couldn’t find any reason for it when looking through the code. Something seems to modify the sort order, but I can’t see what.

I thought that they had gone out of order when I ran an upgrade, as the messages that were out of order were generally much older, and had previously appeared in an expected place. When I fan the SQL above all seemed well, but then the other week a couple of brand new posts have also now appeared out of order. I think the posts it affects are always replies to another post. eg:
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I guess question-answer modifies the sort order, but that should only affect question topics, not general ones.