I migrated my Pantone Solid Coated from CS5 and have all the color settings the same in terms of color management and am still getting the breakdown differences.
One thing that's different in CS6 is the solid ink libraries are now always Lab definitions. As far as I can tell unchecking the Ink Manger's Use Standard Lab Values for Spots never has any affect. Even if you load the older libraries the CMYK conversions from a solid ink color will be color managed and the CMYK values will change depending on the document's CMYK profile.
If you really need the legacy CMYK breakdowns you might have to use the old PANTONE solid to process.acb library, which is defined as process CMYK and uses the same CMYK builds as the older PANTONE solid coated library.
Peter's suggestion nailed it and got the same values. The Illustrator method on the help was what I needed. I was accustomed to making those changes to my /Applications/Adobe Illustrator/Required/New Document Profiles, and it would seem Illy prefers the ones in ~/Library/
I'm fine with using LAB definitions if that's what they want to do. I just don't want the same spots to have different LAB definitions from version to version.