Might be specified in a style that is not currently in use.
I'm having a very similar problem at the moment - every new file I open (regardless of the settings) tells me that the cyan swatch is in use. Even if I have done nothing but start a new document. There is nothing in the file or the master document - but when I print I get a blue dotted line accross my document - and I can't figure out why!
This was just discussed in another thread this morning. Turns out that cyan is the default color for the new paragraph shading feature in CC 2015, so it is always in use.
Turns out that cyan is the default color for the new paragraph shading feature in CC 2015, so it is always in use.
I posted what I think is a fix in the other thread: With no documents open, delete all of the swatches except for the required [Black], [Paper], [Registration] and replace with [Paper] when prompted. Make your own default swatches. Now the Paragraph Shading default swatch is [Paper] for new documents and all non required swatches are selected on Select All Unused.