I did a fresh install of the ML code on a 5D3 with 1.2.3 firmware. I loaded the ML files onto the root of my CF card, and left my Eye-Fi Pro X2 16GB card in the second slot. The install wouldn't complete and the camera appeared to be bricked. 
Fortunately, once I removed the Eye-Fi card it came back to life and booted with ML intact. Oddly though, if I try to replace the Eye-Fi card the same thing happens - no boot up. Swapping or removing CF cards has no effect - it seems like the Eye-Fi card is just incompatible with ML. Uninstalling ML and I was able to boot with the Eye-Fi card in place again.
Fortunately, once I removed the Eye-Fi card it came back to life and booted with ML intact. Oddly though, if I try to replace the Eye-Fi card the same thing happens - no boot up. Swapping or removing CF cards has no effect - it seems like the Eye-Fi card is just incompatible with ML. Uninstalling ML and I was able to boot with the Eye-Fi card in place again.