When you say you've saved the spot color in your library did you actually save a .ASE (Adobe Swatch Exchange) file?
Usually when I add a CutContour swatch to Adobe Illustrator I'll start a blank document and then delete all the default colors out of the Swatches palette. Then I go through the usual steps of defining the CutContour spot color. I usually have things set to where that's the only color remaining in the palette. At the fly-out menu I'll select "Save Swatch Library as ASE..." I'll usually give the ASE file a "CutContour" file name. Once the ASE file is saved it will show up in the Swatches menu under "User Defined." I can close the blank document, start a new AI document (or open an existing one) and that "CutContour" swatch will be available to open or add to the existing swatches.
I don't recall ever having any problems of the CutContour spot color changing to a process or RGB color when re-opening a file, even on another computer running Illustrator.