Something strange going on, Jimmy. I've converted many hundreds of ePub files to Kindle format, and never had the problem that you describe.
Are all the books causing problems from the same publisher, or ebook store, or do they have anything else in common?
Have you tried converting to AZW3 format, rather than Mobi? You won't be able to email it to your Kindle, but it's a more more capable format for sideloading.
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