I don't know why you would need to convert to RTF. If anything, I'm wondering if you've got something weird going on with the way your Calibre settings are configured.
How about trying this: get the "Modify ePub" plugin. Select your epub, run "Modify ePub" with these settings:
Encode HTML in UTF-8
Add/Replace Metadata Jacket
Update Metadata
Remove non dc: metadata elements
Remove legacy metadata jackets
Then send the epub over to your Kindle. See if that makes a difference.
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