Another one here with the same problem.
The guild i want to select is the 4th of 4 guilds i am in, and the only one that will not stay ticked.
I have created a new guild in slot 5 just in case it was a " last guild joined" thing, tick does not stick.
Addendum.
Tried it in Armistice Bastion - no.
Tried it in LA - no.
Tried it in Home Instance - no
Tried it representing another guild - no
Tried it representing no guild - no.
Do not even need to close the WvW window, just changing tabs clears the tick.