Just ran into this issue as well, and I'm almost certain it's a bug. The problem definitely occurs if the file started as RGB and was later converted to CMYK. It makes no sense as far as I can tell, and is something Adobe should adjust. Even after converting the objects to CMYK, and after converting the entire document to CMYK, the black still wouldn't change to 100% K. Only workaround without making an entirely new document was to make a 100% K swatch which Doug pointed out. After doing that once, the CMYK values for black will change to whatever you'd like them to. WEIRD.
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