There is a big bug in the 5D Mark III card handling system.
I report the bug long before the 5D Mark III hit the market but nothing happend.
The same CF cards work perfectly in the 1D X.
I had an err80 with my 5DMKIII two shoots ago and after taking out the battery is was away. After the last shoot I put my Lexar 32GB proffessional 800x in reader and Windows7 said it was a new card and wanted to format it. I put the card in a USB Lexar reader and to my relief there were still pictures on it.
Browsing the pictures I noticed that I was missing pictures and after checking I was missing the last 100 ones. I got 651 RAW pictures and that was 16GB on data still on the card.
I used Recuva to see if the missing pictures were there but there were only the deleted files from previous shoots.
Luckily I write JPG (S1) to my EyeFi SDcard (8GB) that transfer to an iPad with Shuttersnitch so I still got those. Setting for the two card: Rec. separately.
My observations; this was the first time I used the CF card as playback, picture on the LCD, and this because I got a err80 the shoot before. The camera did not produce any errors during the shoot and silently switched over to the SD card as playback medium. The pictures still present on the CF card is half the size of the total size of the CF card.
After saving all the files I put the CF card back in the camera and took more pictures and it functioned perfectly again.
Checked now with Windows7 if there are any bad sectors and there were any.
Next shoots I will have to check during the shoot if the playback setting silently switches and carry extra CF cards with me to exchange the used CF card when this happens again.