Thanks Mike, yes I think I may have been editing out of gamut colors.
I was using this image here
http://www.smugmug.com/img/help/calibration-print-1400-2.jpg. The only issue I saw really with the PP profile was that the car was not a perfect red on the print.. it seemed a bit orange/oversaturated. The man's skin tone was a tiny bit off as well, not by much. Everything else I can't complain. brightness, colors, grayscale were all very good. Profiles done with the Munki are spot on (on the softproof), but I like I said there are situations where Profile Prism is good to have. 4x6 or 5x7 papers come to mind. Love it for my scanner too !
I was able to correct the print by adding adding two clicks of yellow in the Profile Tweak Wizard. The resulting print of my edit using Profile B perfectly matched the soft proof of Profile A. That's what led me to think something may have been missing from the profile editor. My edits did change the soft proof but in a very bad way.
I may have simply been seeing a difference between how PP and the x-rite software deals with out of gamut colors. I may have not seen these issues with normal, real-life images.
My monitor is calibrated using Argyll. 110 cd/m, gamma 2.2, at native white point (6400K in the case of this monitor, didn't think it was worth changing the WP via the profile). I ran argyll with about 2400 patches, the profile should be pretty decent
I typically don't completely rely on soft proofing, I just use it to get an idea as to which rendering intent will give a better result with a specific image. I've always had far better results with Perceptual when using PP.