Well,
same old story...with every OS upgrade a new or revised RawCameraBundle file is provided and this, at least in my system, is causing the colour shift.
I had this problem since the very first serious Aperture 3 ugrades, my Canon 30D images were horribly magenta-shifted, no way to change them back properly...well, maybe with an insane amount of extra work.
So I keep the "good" RawCameraBundle file in a folder (it's version 3.0.1) and at every OS upgrade I delete the new RawCameraBundle file, put back the new one, restart and everything's fine again.
The last upgrade for me was OS 10.6.8, it installed the RawCameraBundle 3.7.1 (RawCameraBundle file is located in Library/CoreServices folder)...I decided anyway to open Aperture...I displayed an image from Canon 30D....for a while it was good then suddenly (when reprocess starts with the new engine) skin tones were shifted to magenta...ok then, deleted RawCameraBundle, put back the old one, restart, launch Aperture 3, the image was good.
Honestly I don't know how far I can go with this, I mean I don't know if Lion will allow that or if the RawCameraBundle file has been changed again.
Maybe you could check the Lion version of the RawCameraBundle file, I bet that is not 3.7.1 anymore.
Maybe is this causing your colour shift problem within Aperture 3, maybe not...You can try...if you have the old RawCameraBundle file; I think you may retrieve it easily from a Time Machine backup.
Bye!
Alberto