Yeah, disconnecting forces a 1 minute interval where you cannot log back into the same character. If you don't log out properly, which takes 30 seconds, you are forced to wait 60 seconds for the server to log the character out. This was to prevent people from disconnecting manually during fights, to allow them to force a logout in 30 seconds, when a monster would kill them after 40-50 seconds, and would interrupt their logout attempt. It used to be a 30 second wait in the first year or two of the game before they extended it to 60 seconds on disconnect.

It actually takes less time to launch PlayOnline Viewer and navigate the menus than it does for the server to disconnect you. I've disconnected because my ISP had trouble, relaunched FFXI, made it to the character select, and been told my character is still logged in and that I have to wait until it finishes logging out.

Being disconnected by your account being logged in on another system forces a disconnect and 1 minute wait as well, to give you a chance to react before someone can dump your items, which was the intent back when account hijackings were more common.