I had the same error, and the template definition in style.css didn’t seem to matter.
Going to the admin portion, I went to change the theme, and had 4 different errors pop up on the theme change page, all about permissions.
I logged in via a SSH session, and in the wp-content directory, did
chmod -R 755 themes/
And the permissions fixed all the errors, and my comments are now back.
Silwenae
