Perhaps you could post a sample of such an epub so people can take a look at it. The only time I've seen anything similar to what you are describing was where the .opf file had scrambled spine entries and the program I was using organized them into that &*()_$ order.
Quote:
A spine
As its name indicates, this is a “backbone” where the reading system finds the default reading order of all publication “chapters”. As these sections of a publication may not really represent book chapters, each item of the sequence is called … a spine item.
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BTW, I do not personally use any of the manifest items. You did notice that
Add unmanifested files to manifest and
Remove unmanifested files from ePub are mutually contradictory.
Much the same that
Removing margins from Adobe .xpft files doesn't make sense when you also have
Remove Adobe .xpgt files and links checked.