Changes in this release:- Workaround for calibre "bug" to ensure that if user has both remove javascript and smarten punctuation checked, that remove javascript runs first which ensures smarten punctuation will actually work correctly for quotes.
I've emailed Kovid about the issue with an example epub as it looks like an issue with the smarten punctuation code in calibre. I'm sure some of you might have hit this unknowingly as I have - you go to read an epub that you "thought" you had done smarten punctuation on, but are still getting the straight " quotes in it. It looks like if there is an edge case (found with Baen books in my case) where javascript blocks in the html will interfere with the smarten punctuation logic. While the javascript is present, quotes will not get converted.
In the case of Modify ePub, if you have both "Smarten punctuation" and "Remove javascript" checked, then it still took two passes, because of the order they executed in. As a workaround I have now switched them around internally, so if both options are checked your books should end up "smartened" in one pass regardless of whether Kovid decides to change the calibre behaviour or not.