Problem: Filters should be applied in a certain order. This can be set by ordering filters on admin/filters.php. (http://docs.moodle.org/dev/Filter_enable/disable_by_context#Getting_filter_configuration)

Problem:
In lib/filterlib.php:filter_get_active_in_context filters shoud be returned due to their order. Since the loaded filters are stored in an array with the name of the filter as key. Ordering of filters get lost.

For us this causes a problem, since our Moodle can be reached from multiple domains. We have a text filter that changes the URI to an absolute URI which is relative to the basis URI (e.g. www.domain/admin/index.php to /admin/index.php). If now the media filter is applied first and afterwards our filter (name: wwwsso) is applied, the media filter will create script tags for the flash player with the full domain and our filter will afterwards remove the domain. Finally, the media player cannot load the file.