Whoops - I just noticed that you have two Mark iis --- the below won't apply directly to you - but I guess I'll leave it in case someone else finds it in a search
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Of course I can't be sure -- but I had what would seem to be the same symptoms, (Canon FM 1.1.3, ML) and I couldn't read or format CF cards in the camera. Even with no ML - still no-go. I tried all the pin checking and rebooting I could think of, and was getting ready to send it in to Canon. THEN I found the recent 5D Mark iii ML for Canon FW 1.2.3. I installed it, and went to the ML Menu to enable the CF card workaround - and, now I can read and format and use all my CF cards. Will try to understand the situation and real causes better - but, for now, I'm really happy to be back in business. Good luck with your situation.