I have Photoshop CS5.5 with the ACR update for the Canon EOS 5D MKIII, and i have been able to successfully load images into it, but after my latest shoot, it doesn't want to open up the images properly. I selected all 400+ images, and when i dragged them into photoshop, or selected them by file/open, then came in as though they were jpegs, and completely bypassed ACR. Now when i tried selecting the images in a group in Windows explorer, and selected open with..., it opened them individually in ACR, so instead of their being the image scroller pane on the left side of the screen, the first one came up, and then when i pressed done or cancel on that one, the next image loaded up in ACR. So what's going on with ACR?
Use Bridge. Locate the folder with the images in, and work from there. You can load multiple RAW files into ACR from Bridge, and Sync them, but you'll run into trouble with system resources.
Cr2 files should not be doing what your saying. However if your shooting in raw+jpg mode, it seams feasible that it may use the jpg image instead of the cr2 file, especially if your camera is newer than CS5.5.
You know what happened, I was playing with the HDR mode of the camera, and I didn't realize it shot each individual in RAW, then converted them to JPEG later. So when i was bringing them into PS, i chose all the images, including the JPEGs, so it makes more sense now why that was happening. Thanks!