- What file type are your Illustrator files?
- Don't apply a color profile to them.
- Do you use transparency?
- Did you check if the color blending mode of the document is CMYK and not RGB?
1. file type is 'Adobe Illustrator Artwork 21.0
2. A Colour profile hasn't been applied
3. Transparency isn't used
4. the colour blending mode is CMYK on both files
Its weird because this never happened on CS6 and I am using the same files.
This is fine but doesnt make sense to me as the CMYK working space is already U.S. Web Coated (SWOP) v2 so I don't understand why there is ever a change in colour.
Your Color Settings Working CMYK space is never used to color manage existing documents unless there is no CMYK profile assigned to the document (Discard (use current working space) is selected in Assign profiles...).
This is a common misconception—in most cases Color Settings is an application and not a document preference—Color Settings only affects how future documents are setup.
In your case the CMYK Illustrator file has no profile assigned, so the InDesign document's assigned profile is use to color manage the Illustrator file. Any change you make to the document's assigned profile will change the appearance of both the placed AI file and InDesign native CMYK colors and swatches.
if it were only that. Sigh.
Color Settings is an inter-application preference when it comes to different versions of InDesign started on the same machine. ( And here on my Mac Color Settings is not synchronized through Adobe Bridge for PhotoShop and Illustrator )
Change one thing in Color Settings when you run e.g. InDesign CS6.
Then quit CS6 or leave it open, doesn't matter.
Start CC 2017.1 on the same machine now.
Go to Color Settings and you'll see that the change you did with CS6 is visible also with CC 2017.1.
Change something in Color Settings with CC 2017.1.
Switch to CS6.
You can see the change there as well.
Tested with Mac OSX 10.10.5.
Color Settings is an inter-application preference when it comes to different versions of InDesign
Yes, but my point was changing the Color Settings' Working Spaces doesn't affect the way an existing document is color managed unless the document has no profile(s) assigned—either you've removed the profile(s) via Edit>Assign Profiles>Discard (use current working space), or the document was created with the CM Policy set to Off.
Syncing Color Settings by any method wouldn't change that concept.
This is fine but doesnt make sense to me as the CMYK working space is already U.S. Web Coated (SWOP) v2 so I don't understand why there is ever a change in colour
The OP is assuming the CMYK Working Space color manages the document, but it's actually the assigned profile and they can be different.