I can't remember if font color was one of those things that required publisher settings to be enabled...I don't think so. I would check the epub file with your favorite editor (Sigil/Calibre are the 2 I use) and see if there are some hard-coded colors in there. One of the major offenders is smashwords. They actually tell their authors to hard code the text color to black (because that is what looks good when it is printed I assume)...but totally breaks the ebook.
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