if it was something wrong in NEI ... I would expect the force hard update to fix it. Also happening in both launchers... Maybe something with Java? I can try to see if there is an update. It has happened to me in the wild...don't really even have a base yet. For me it happened...I managed to get back to spawn....TP'd out into the world looking for a base. Picked one and it happens there when trying to break blocks as well.
So after a long testing with @codeljack we found out that the world was corrupted as the issue was only in the rwg world. I now did a rollback of one day of the world and it is fine again.