One guess I can make is that maybe before your software upgrade there were some defaults being applied to your RAW files on import(sharpness, clarity, vibrance, saturation) that aren't being applied anymore with the software upgrade and new camera body. Do you still have your 50D? If you could do some fresh test shots with both bodies and bring those into your new software you might get an idea what's going on. I'm no expert, but I think a RAW file from either camera with all settings wiped out is going to look a little soft, not very saturated, and maybe even a bit under-exposed. I know the screen on the 60D is a lot brighter too, I turned mine down because it was making the shots look a lot brighter than they were. Those are just my thoughts, hopefully some others on here can chime in and help out as well. The 60D thread is a great bunch of helpers! 