I've artwork in Illustrator that's a Grey gradient sitting on a red background - overprint is turned off for the object.
Document Colour Mode is CMYK.
0 White - 60 Black - 0 White
In illy even the seps show it as 4 colour.
I'm importing the artwork to InDesign to be litho printed eventually - but I can't seem to get the gradient to operate in grey only.
Try making a new Illustrator document that starts out as CMYK.
I was able to duplicate the problem by starting a document as RGB, then changing it to CMYK.
All the Greys show in the pallet as black only, but separate into 4 colors.
(The rule in this screen shot should be 100% K, but still shows with the black channel turned off.)
A brand-new CMYK document worked as expected.
Aw jeez - guess you're right. That's very confusing.