Quote:
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You probably have (more) code somewhere (could be the CSS or the document itself) that sets it to Blue
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You are right.
To check that I exploded a book pre-Calibre conversion (epub to epub) & post-conversion & compared the 2. Calibre introduces a few CSS attributes & <span>'s with "blue" in them, which were not there originally. So, even if a book gets correct colors being converted once, it reverts to blue on any further conversion.
I would consider this a
BUG.
In any case, I go back to tweaking epub in Sigil & converting to mobi in Kidlegen or Mobipocket—it is much easier.