You could try do update ahead of time since there's another way to it. On the 1st menu before you log your playonline, there's Check Files menu. Then after you select FFXI application, it will recheck and report how many files need to be updated.

This way of updating are even more slower (like 5-10 minutes longer) compared with the one after you logged in since this method literally checks every files in your installation, but at least you can run this when you're not in active subscription or doing this on another computer.