I finally managed to get my per-pixel lighting working, so I just had to post a screenshot 
http://studenti.lboro.ac.uk/~cojc5/Vecript/07_Aug_2003.png
After much tinkering it finally works correctly, although I’m not sure how depth layering should affect the lights - at the moment i’m thinking that anything in front (closer to the camera) than the light should not be affected by it, but i’m open to suggestions.
I’ve also noticed that Swing seems to loose its icons and not be able to restore them - both the icons on the JTree and the texture for the scroll bar both dissappear occasionaly. It seems to be related to resizing the GL canvas, but i can’t see anything i could be doing wrong. Is this a bug of Jogl? Has anyone else seen it before?