Just wanted to put this somewhere:
It seems that the auto-logout feature is disabled when you are in an active crafting stance (have your anvil out for BS, etc.). Now, I may be mistaken, but I discovered this by accident yesterday. I wanted to make a bunch of lumber, so I set it to auto synth, then alt-tabbed to do some stuff. Well, Counter-Strike caught my attention, then after quite a bit of counter-strike, I realized that my FFXIV was still running. I maximized the screen, to discover that I was still logged in, with the auto-synth window open telling me how many success and failures I had.