In Joomla! 1.5.8 and later, a default filtering choice is in place for those who have not selected an Article Filter option. The default applied for those who have not made a selection implements "black list" filtering as a security precaution against possible XSS. In version 1.5.8, all users, including members of the Super Admin group, have this set by default. In versions 1.5.9 and later, users in the Super Admin group do not have any filtering by default.

Due to this change, you might notice problems trying to save a Youtube video, or embedding other Javascript or Flash objects into your Articles.

You can read more about it and how to allow scripting in your content, by reading the followin article on the official joomla docs

http://docs.joomla.org/Why_does_some_HTML_get_removed_from_articles_in_version_1.5.8%3F