After editing a topic, when you go to save it, the Headers and Footers dialog sometimes pops up asking if you want to apply this change to all topics using this master page, even when you have not changed anything in the master page.
This happens to me more often than not.
I am using Windows7, 64 bit, and working on legacy projects upgraded (opened and saved) to RH9.
I have also seen this...back in RH8 too. (Currently using RH9-HTML, Windows7, 64-bit, and working on legacy projects). I just thought it was my inexperience doing something wrong. I can't seem to find a pattern to what makes it happen.
It's not you and I wish I had an answer.
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See www.grainge.org for RoboHelp and Authoring tips