It is possible that you have an unnamed color in the file, and the IDML regenerates it.
That is the default colour for the paragraph shading, for some reason this default paragraph shading colour makes it always back to an idml, you can safely ignore it.
That's exactly the reason.
The paragraph shading is automatically assigned the Cyan colour. When you rebuild a document using IDML - it has to give the paragraph shading a colour - and therefore assigns the Cyan.
But it's no harm - if you're not using Cyan in your file then there's no harm.
see that rather lengthy discussion here:
Larstown Jun 23, 2015:
Some solutions revolve around using scripts that change the default of the used color of paragraph shading to something else.
Rob Day provided an AppleScript solution, I did my version in ExtendScript and recommend to change the default color to a tint of 20% of [Black]. See my script here in reply 35:
You have to run the script when no document is open.
From now on the shading color is 20% [Black] by default.
But that does not mean, that if you open older documents, that the default automatically changed there. Only for documents that you are building from now on. And it also does not mean that the unwanted color will not be copied over, if you are using documents from colleagues and copy/paste contents to your own documents.
I discovered another oddity.
Even if you manage to change the default to 20% [Black] for paragraph shading, it could be, that if text is copied over from a different app, InDesign is adding "C=100 M=0 Y=0 K=0". Even if the copied text does not contain this color.
To workaround this I posted a solution where you have to change the option of InDesign's Clipboard Preferences from "Text only" to "All Information" and then "Paste Unformatted". See also my replies 36 and 37 here: