Yellow boxes behind all caps text

I had a Quark 6 Mac file converted to ID CS3 Win using Q2ID and when I opened it I replaced the fonts with our own, however wherever the text had the all caps feature used in Quark (I guess) there are yellow boxes behind the letters. I can get rid of them only by selected the text and clicking off the All caps (TT button).
Is there another easier way to keep them as all caps and get rid of yellow boxes?

You have highlight substituted glyphs enabled in your composition
preferences.
Bob

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