Mitten, after approx what length of time did the ultrasound hurt your knee? (hope physio didn't continue with it? 
You can heal fractures with US - the more expensive units have different wave patterns to do this.
Generally you shouldn't feel anything on US, possibly a bit of heat, but most patients feel nothing.
Tuning forks have been proved to be unreliable sources of detection for stress fractures. US is more useful than xray according to recent studies where real stress fractures were identified with MRI.