🚀 go-pugleaf

Speculative answer based on things I half-remember: sometimes Word text is coloured because of a font-style, sometimes it's coloured because mark-up from track changes is being rendered as a condition. When the text you import drags a condition with it, you can change/apply FrameMaker paragraph definitions till you're blue in the face :-}

Take a look at some text with a problem colour; put the cursor in the text and see if there's any indication of a condition in the status-bar. The keyboard short-cut for "clear conditions on selected text" is esc, q, U - thanks, Arnis!

Simply importing the file is almost certainly a bad idea, but you've decided that already. Other contributors will probably have more to say about the different strategies for getting clean, usable, formatted content out of .doc files. fwiw, ymmd, and for documents without tables: I use a Word macro to tag each paragraph with its style-name, then save as text and import the result as MML.