Glad that helped! FoCal changes several settings, but I wasn't aware that was one of them. Often there's an option to restore camera settings after a crash, sometimes not, though.
Yes, I use back button AF exclusively. Only time it's an issue is if you hand your camera to someone else. On the 5DIII, though, you can just set it to green square/A+ in that case (no full auto on a 1-series). As you learned in troubleshooting your issue, that mode cancels out customizations like back button AF (but it still shoots in RAW if that's how it was set).