I’ve just tested Rebranded Meta Widget and it doesn’t change anything on a test site using Arclite template (133 themes pack). I thought this plug-in would replace the link to WordPress.org on every site but it doesn’t. I’ve not checked with other themes. Are you using it on edublogs? If yes, you have some problems too. This blog links to WordPress.com, this one to WordPress.org, etc.
Thank you for feedback.