I tried many ways of formatting in camera, adding files, copying folders manually, using my Mac Air to format, and found a solution.
Last week I tested this and it works perfectly, so long as I did not mix up the steps.
This works fine on my 6D camera, I don't use CF cards of a different camera, but it should also work fine.
1 Place SD card in PC / MAC, and format to EXFAT (single partition)
This is something the camera cannot do.
This allows for large files over 4gigs.
2 Place in camera and AGAIN format in camera (this creates flagged DCIM and MISC folders)
3 Place the card back in PC / MAC and create a new folder (any name) ***Put everything (media docs etc inside this folder ONLY)
4 DO NOT PLACE files on the root, this will cause the camera to not read the card at al!
I have 70+gigs of media on one of my 128gig cards and I have room for over 2,000 more raw files. 
*** NEVER FORMAT YOUR CARD IN YOUR CAMERA NOW*** You will lose everything by formatting it, including your other media.


