Although this wasn't so obvious since it
only showed up for factory settings and in the preferences window.
Panel display order depends on registration order,
Sorry for the noise. On the bright side we no longer need to move
classes around to re-arrange panels.
ui/ --> startup/bl_ui
op/ --> startup/bl_operators
scripts/startup/ is now the only auto-loading script dir which gives some speedup for blender loading too.
~/.blender/2.56/scripts/startup works for auto-loading scripts too.