This was discussed in http://moodle.org/mod/forum/discuss.php?d=31804 and mentioned by Martin in
MDL-3313 (that bug is closed as it's not exactly the same bug as this) but I notice that many themes still use $CFG-theme instead of the function current_theme(), thus some of the logos etc. don't work if the theme is used as a course or user theme.
Suggested fix, at least for the themes
and all of the standard themes
change the use of $CFG->theme to use current_theme().
Lot of the instances (like for the standard themes) are for the favicon.ico, so it's very minor, but still. Formal_white is quite broken as a course theme as the Moodle logo is missing.