In Moodle 2.0 legacy filters only work within a course. For a filter to work outside of a course, in messaging for example, it needs to be updated. Discovered as part of MDL-25240.

At a minimum the filter needs to include a class that extends moodle_text_filter similar to this:

class filter_moodledocs extends moodle_text_filter {
function filter($text, array $options = array())

}

It also most likely requires a lang directory to contain its strings. Typically filters only require a single string.

$string['filtername'] = 'Moodle docs';