I believe that others have managed to upload pdfs directly by adding 'pdf' to the list of allowed image extensions in the HTMLEditor/editor/filemanager/connectors/php/congig.php file. I haven't managed that, - which is probably an error on my part - but if I click the 'Insert Image' button then 'Browse Server' and in the file manager (resources browser?) I can click the browse and upload buttons there and upload pdfs with no problem. I can then link to them easily.
I'm not sure why you are getting the 'upload unavailable' message assuming that (if you are using the latest version of HTML Editor) you have clicked the 'customise' button in 'Global File Uploads', ticked the 'Enable File Management' box, and that you have given permissions to the specified uploads folder.
I had a problem a while back when I was making adjustments to the HTML Editor instance in the PowerCMS folder (which contains it's 'own' HTML Editor folder) but the changes were being made to another configuration in the root folder.
All I can think of to suggest is to recheck your Global File Upload settings, make sure that the changes are being applied to the correct HTMLEd files, your uploads folder - as specified in the Quick insert window - exists on the remote server and that the permissions have 'stuck' - and that all of your HTMLEd files have been uploaded.
Hopefully someone who has had a similar problem will post their solutions.
