I noticed that with SpeXtrum earlier and thought it was due to misreading of the input. I was about to start trying to debug that!
So thanks Tanas - you've just saved me having to do that!

It is possible to change the joypad mapping so that the xbox buttons represent spectrum keys rather than the joystick. At the moment you'll have to edit the mappings.xml file.
At the moment the thumbsticks can only really be mapped to joystick movement (I've forgotten to include mappings for the separate thumbstick directions...DOH!). But it is still possible to have say the left thumbstick mapped to joystick movement, A mapped to joystick fire, the d-pad mapped to (for example) Q,A,O and P, and X, Y, Z, Black or White mapped to other keys.
This way the majority of control options are catered for. If this seems like a good idea to people then I will make this the default setup in future versions, so comments please!
Ultimately the controls will be definable from within the UI, I just haven't gotten round to that yet!
Carch