I did see the images / screenshots.
CR/LR is taking into account the crop factor of the 20D correctly. I have checked it personally.
The distinctions you are seeing between the two profiles for the 17-40 are actually due to an internal issue with how Adobe built some of the initial lens profiles (i.e., based on measurements captured at a single distance only). It is not because CR/LR is not taking into account the crop factor.