Hi Jason,
Thanks for the reply. Since I last posted I had a look at where the file manager is defined in the .js file and found that the last two lines had 'false' instead of 'true' for file manager, so changing to 'true' fixed the problem.
FCKConfig.ManagerEnabled = true;
if (true) {FCKConfig.Plugins.Add('kfm');}
Simple! Now that I know this is all you have to do, it's no longer an issue for me. However, it means that the wizard for creating the HTML editor is not writing the correct entry so you may want to look into it in case you are inundated with requests for help!
p.s. Thanks for a terrific plugin.