Final update.
From X-Rite:
The profiles are obviously valid because WHCC uses them to print with and you can use them in Adobe products as well as iPhoto. This could be a profile version issue. Some applications (i.e., CS5, Lightroom3) support both Version 2 and Version 4 profiles. If WHCC created a Version 4 profile and Aperture 3.1.1 only supports Version 2 (you will need to check with Apple on this version of Aperture), then you will have your answer. Perhaps Aperture doesn’t support custom ICC printer profiles??? WHCC is correct…this is an Apple issue that you will need to address with them.
From WHCC:
I don’t believe that how the ICC profile is created or by which program it comes from has any bearing on how other programs can use it. Take JPG files for example… you can make JPG’s in a variety of editing programs. As long as a JPG is a JPG, it is a universal file type that will be able to be opened and used in any program that recognizes and supports JPG files. ICC’s should be the same. If the program you are using can recognize and utilize the file type, they should work universally. There is nothing Photoshop specific about them. If other applications on your computer can see them (ex, iPhoto, Photoshop), then they should be installed correctly and the reason Aperture can’t identify and use them would be an Aperture support question that you would need to talk to Apple about. I apologize but that is all the information I have on this at this time.
Conclusion:
After doing a "Save as..." for a WHCC profile & placing it in all three ColorSync/Profiles folders & getting nothing, the problem is either in our set up/system. Or an Aperture bug. I tend to think the latter but then I can't believe WHCC hasn't heard about this before.
I also tried to tell what version they are and they indicate 2, 3, and 4 in ColorSync Util.
So I'll try to forward all this on to Apple support & see if any update happens in the future. I'm not crazy enough to think they'd actually respond with an answer
I did also direct Tweet Scott Bourne who like Apple rarely responds. But given his professed love for them as a sponsor & his personal connection, I'm a bit suspicious that he uses them as much as he says if this is a general bug. It would make it awfully hard to get prints correct as his pickiness would want. This is another reason I don't have much hope that it's a general problem.