Do you have access to software which can save your RTF as HTML e.g. MSWord. If you examine the HTML file in a text editor you may get a better idea of what's going wrong.
Alternatively, if you use the Convert - Debug feature, you can capture the HTML which Calibre extracts from your RTF during the conversion to MOBI. This will also help you diagnose the problem. I usually find the HTML in the Debug Input subdirectory the most helpful.
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