Just back from a small vacation in San Francisco and I noticed immediately the same dramatic darkening problem after rendering the RAW generated by my brand new Canon 6D. I'm using Aperture 3.4.5 and the last Digital Camera Raw 4.0.6 so everything updated to the last release.
I also checked the Highlight Tone priority and this was disabled so this is not the point.
I made a test because I was curious to understand if this was a general issue of this Aperture release or if it was related to the RAW generated by the different Canon cameras so I went to check if the same darkening problem was happening on the old Canon RAWs created by my older Canon 40D and to my surprise the darkening problem is not happening.
So this issue seems really linked to the RAWs of the 6D and like suggested in the former posts could be linked to the OS X Raw conversion and not to Aperture in itself.
Pretty frustrating at the moment... especially because the JPEG generated by the 6D are excellent (moving from the old 40D the improvement is amazing... ) and after the rendering of the RAWs all the pictures become definitely underexposed...
I don't even consider Lightroom because I find it really awful compared to Aperture but this rendering issue is a top critical item for being able to use correctly Aperture.
Ubaldo