I've been getting this same corruption on files from my 1DX as well. At first I suspected the CF cards but not any more!
For me, the problem ONLY occurs when I transfer files directly from the 1DX to my PC using the camera's built-in usb socket and the supplied Canon usb cable. I was seeing roughly 10% of my files corrupted. This was such a problem that I would have to record images to both CF cards in order to, hopefully, obtain one uncorrupted copy. This worked but severely reduced the number of available shots as I was using one 8GB and one 16GB cards.
However if I remove the cards and transfer the raw files onto a backup device first (a Nexto extreme, http://www.nextodi.com/product/eXtreme_en.html
) I do not get a single corrupted file. NB. I can then use the same usb cable to transfer from the Nexto to my pc, hence ruling out the cable as well.
Could you guys please see if you can confirm this by using a card reader, or backup device, to take your files off the cards instead of the usb socket on the camera??
If we can trace the problem to the usb socket we will have something to go to Canon with.