@JSWolf - it is because you ticked multiple options, the xpgt one found that a file needed updating to remove some html from it, and then the insert cover cover one chose to delete that same file at the later step in the pipeline. They then conflicted when it came time to write the results back to disk at the very end. I had fixed it but not bothered pushing another beta out to see if I could get away with it, obviously not...
If you just want to test the covers functionality, then only select that option (until I push the new beta out). I'm still in suspense over whether an ePub modified by this plugin solves your iBooks issue.
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