The MPART_ALT_DIFF rule gets triggered when the text in your HTML and text variants of an email are sufficiently different (This doesn't pass the suss test: in general, you'd want these two variants to have the exact same prose!)
One extremely common reason this rule may be triggered is if you're attaching a text or HTML variant of your email that is actually blank. It's better to omit a version entirely than to include a blank one!
Want to learn more? You can find the full list of SpamAssassin rules
here, or the source code for this specific rule
here.