This sounds very much like the underlying format is a PDF, they can convert to word and look fine but won't convert well at all to mobi.
My best suggestion is to convert from RTF to RTF using calibre and in the tab Heuristic lower the default 40 to say 15 then see what the new RTF looks like. Then you will need to tidy up the new RTF manuall. That means removing any headers and trailers and manually lifting the text where the gaps are. It's a painfull and long process but it's that or locate a mobi file or DRM free ePub you can convert to mobi.
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