<What the ducks says is spot on. However I am curious that you believe that runnin some Modify ePub functions is creating the issue and that it does not exist in the original ePub. If you ever hit this issue again, please PM me a link to the original ePub and the modified one along with as above what options you had ticked.>
Kiwidude, I didn't know what was causing the problem and didn't know where to start looking. I just noticed that it ONLY happened after I ran Modify ePub, but not when I ran Calibre's conversion program. Next time it happens, I'll look at the before and after OPFs to see what the difference is. TheDucks' answer makes complete sense to me. I'll post my findings (or if I can't figure it out, I'll PM you with links). Thanks. And thanks for Modify ePub, too. It makes cleaning up epubs less of a chore.
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