I'm sorry if I broke the rules. Google brought me here by "Illustrator" keyword. I thought my answer might be useful for those looking for the answer to the question applied to Illustrator, as well as also be applicable to InDesign.
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I had this problem in Illustrator. Eyedropper options box is a little buggy. Appearance was checked, which should mean that all appearance settings are being picked, but when I twirled it open, there were unchecked boxes.
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