Hi Walter,
Thanks for your answer.
I think I have half-solved the problem.
Here is the problem in more details : on 5dMIII, when I format my CF cards in ExFat with Disk Utility in El Capitan, I have multiple options to choose (GUID Partition Map, Master Boot Record, Apple Partition Map).
After formatting with any of these options and re-inserting card in Camera I get the following error: "Card1 cannot be accessed Reinsert/change the card or format card with camera"
However, in Disk Utility you have two ways to format the card:
Option 1: you can select the Type of Disk and Erase it (which gives you the options above)
Option 2: there is a small dropdown that allows you to select the Disk with the name you gave it, and format it. This does not give you any of the above options.
Now, if I format my cards first on Windows, in exFat, then in-camera with the 5d, and then format them using Option 2 on El Capitan, then and only then do the cards work fine on the 5d.
However, as soon as I format on El Capitan with Option 1, then even if I use 5d in-camera formatting and Option 2 straight after, the card remains unusable on the 5d.
One additional note that may help figure out the problem - after formatting using Option 1 and when trying to format on Windows, I can format the card successfully in exFat, but only for 200MB...
So to summarize the solution if you have the same problem as me - never use Option 1 in El Capitan's Disk Utility, only Option 2. If you do use Option 1, then format first in Windows, then in-camera, then Option 2 on El Capitan.
Hope this helps someone.