[Registration] is not a particular color, it's 100% of every color used in the document, so if InDesign thinks for some reason that your spot color is in use, it will be added to [Registration] and the registration marks.
If the color is showing up as a named color in the separations preview it hasn't been converted, as far as InDesign is concerned, into a process color. You said it was converted to CMYK; how was that accomplished? Changing the color MODE in the swatch definition from the swatch book to CMYK doesn't convert the color. You'd need to either change the TYPE to process, or use the ink manager to convert it.
Have you turned off the CMYK plates in Separations preview to see if the spot color shows anywhere in the document? It would appear in black in the preview. Don't forget to look at master page pasteboards which don't generally show on document pages.
You can try doing an object search, as well, for objects that the color. You'll need to do a total of 4 searches to cover the possibilities: an object search for the spot color as fill, an object search for the spot color as stroke, a text search for the spot color as character fill color, and a text search for the spot color as character stroke color. Be sure to include master pages in the searches. If the document is short, the visual method would be faster.
If the color really isn't being used, post back and we'll discuss ways of removing the swatch from the file.
Peter