I was using 3.1 on WP2.6.3 & it was working great. I had written a list of guidance notes for a client who is using it as a basic CMS for half a dozen pages, with TinyMCE Advanced being central to thise instructions. I had used TinyMCE Advanced, as it had worked excellently to overcome all the major shortcomings of the standard visual editor.
When I came to put the site live, I moved WordPress to the root directory of the site. There appeared to be no problems, until the client mentioned that when trying to insert a media link in the visual editor that it would not appear at the cursor position, but instead at the beginning of the page(?!). It was when I was investigating this that I noticed that TinyMCE Advanced is no longer appearing when you come to manage the pages.
It is completely set up as an activated plugin. I can make any changes I want in the settings, such as extra toolbar options. I get no error messages. It is just that it does not appear for use!
Any ideas, as I look pretty foolish to the client right now!