Sounds like an issue with the file conversion. The Sigil suggestion is a good one to recreate the ToC for your books.
I would also try a few other things:
1) Have you confirmed that it is only these converted books? You don't have issues with any other sideloaded books?
2) Have you confirmed that you have the same issue with these books if you sideload them onto the main memory rather than SD card?
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