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I haven't looked at the code to see if it's feasable but have you considered aborting the save-draft ajax request when the post reply button is clicked?

This seems really odd, I've never had it happen. Granted I don't post that much but I post enough to where I feel I would have encountered this if it was that common. In theory it seems like something that would take incredible timing. Maybe you do have an add on that is affecting it although I'm not sure how that would happen. Maybe if you could post a list of your add ons?