[B]Try formatting the card. I had this issue with one of my CF cards. Worried me a bit, but I formatted it to the camera and all was well again. [/B]
Both of my cards have been reformatted in the camera. It didn't help.
What software are you using to download? Do you have it looking specifically for photo files or all files? It may not recognize the CR2 as being an image.
I use Picasa software to download into the computer and then transfer to DPP to process the RAW files. Been doing this since last August without a problem. When I download two images show, one cr2 and one .jpeg.
Now when I download, only the .jpeg shows. When I go to DPP, only the .jpeg is there.
I've personally never really understood the RAW+JPEG thing. To each their own, I guess, but that just takes up so much space on the card...the RAW files are already big enough as it is. Anyway, back on topic...try formatting your card(s) in your camera.
Sometimes I shoot in RAW only. I'm glad I had the camera set for RAW + JPEG this time. I had taken about 50 shots. If I had set the camera to RAW only, I would have had nothing.
I have also downloaded with two different card readers and get the same results with both. I have also tried a fresh fully charged battery in the camera. Didn't help.
Any other suggestions to try.
Larry Q