There are several people who posted (including me) with the same problem. At least one couldn't even update manually. There is obviously an issue with the firmware which is a new format (twice the size). I created a support ticket with Asus. The more that do the better - See: http://www.snbforums.com/threads/rt-ac68u-firmware-version-3-0-0-4-386-43129.72638/post-690649
I just tried a manual update and it worked. didn't try the gui a second time to see if it'll work or not.