<I've used Modify ePub extensively and find it works very well. Next time you have a problem, take the ePub (the one before the plugin was used) and validate it with ePubcheck and see what errors there are. Fix the errors and then when it validates, run the plugin again and see what happens.>
Thanks, that's a good idea. I'll validate it with ePub Check, fix the errors, and run it through Modify ePub. If I see the problem pop up after that, I'll compare the OPFs. That gives me several things to try. Thanks to everyone who made suggestions.
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