Ah, I see how it works now - obvious really but something I'd never realised.
The search box is context sensitive.
If you use it from the home page, then it searches the whole forum
If you use it whilst in a particular sub-forum then it only searches that sub-forum.
If you use it whilst reading a topic, it will only search that topic.
So I guess the key is to only use if from the home page for a forum wide search.