This was an obscure one, this workaround did it for me:
https://community.openatrium.com/issues/node/2561
The Wysiwyg FCKeditor 2.6.6 is not visible when only one input format is authorized for a given user/role, but it is visible when two input formats are authorized. How can I have it visible with only the default input format authorized?
Also discussed here:
http://drupal.org/node/1296012#comment-form