One of the other guilds on our server couldn't register for war this week. Officers had the option to register, but were being told they're already registered (but weren't on the leader board).
What seemed to get around that:
During the war registration window, opt out all players, then opt back in. Now you should be able to register.
The issue seems to be known, but hard to reproduce according to our GS, but I wanted to share this potential work around( server 7, guild Black Sheep. No I'm not in that guild)