Did you enable advanced file management and uploading from within the wizard for HTML Editor? You must ensure that you have these options set and configure the advanced file management options. Make sure to check on the security portion of the advanced file management options and ensure that you have it allowed for the user you are working with.
Also, have you tried putting the files in a zip archive before uploading them? The size restrictions for the zip should be large enough for the editor folder and other files.