Theme colours were getting overwritten on startup with defaults (as in 2.4
system). Changed this to allow changing the default theme, and added a
'Reset to defaults' operator in user prefs. Perhaps next step to look into the
py presets system for themes too (nice and easy to share).
If you're using a custom B.blend you may get some strange theme colours on
startup if they weren't saved properly before. 'Reset to default' button in theme
preferences should fix it back to defaults.