I can't reproduce it using your preferences file and adding lines to your document 'happening.svg' with Inkscape 0.47 (r22583, built Nov 24 2009) on OS X 10.5.8: all nodes snap to grid intersections when using the pen tool in 'bezier mode'.
Puzzling - I don't understand why snapping sometimes fails for you.
I can't reproduce it using your preferences file and adding lines to your document 'happening.svg' with Inkscape 0.47 (r22583, built Nov 24 2009) on OS X 10.5.8: all nodes snap to grid intersections when using the pen tool in 'bezier mode'.
Puzzling - I don't understand why snapping sometimes fails for you.