I've had the same difficulty that icallaci describes with the plugin, but went a little further in trying to figure out how to work around it. I was able to isolate the result to the "Update Metadata" option. For files that will experience the problem, running the plugin with that option checked will cause the opf to fail and Sigil will create a new one in alpha order. If I re-do the process with the same book, and leave that option unchecked, the resulting opf will be acceptable.
Kiwidude - I have pm'd you links to before and after versions of a file that experienced this. Didn't want to post publicly.
Last edited by Barb-B; 03-01-2013 at 02:31 PM.
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