Hmm it may be totally unrelated but I've had something similar recently.
I was converting a PDF to rtf then mobi and placing on my Kindle. When I started reading the document, the text had two shades of grey from paragraph to paragraph.
I opened up the rtf copy I had saved in wordpad and after messing about found it was due to character encoding I think. So I selected the whole doc - made sure I saved the whole lot in the same font and with the same encoding - Western European ? I can't remember but it fixed the problem I had as everything was now the same.
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