Can you help me with TinyMCE settings?

I’ve got an annoying problem with the TinyMCE settings on a 1.6 EE site. I’m trying to get the link wizard to work properly for any URL, but I can’t make it work for both regular URLs and the ones created by the File Uploader.

These are my relevant TinyMCE settings:

relative_urls : false,
document_base_url : '/',
remove_script_host : false,
convert_urls : true,

These work fine if you enter normal http URLs in the popup TinyMCE link wizard. But if you try to enter a URL generated by the file uploader, e.g. { filedir_18 } myfile.pdf the generated HTML is incorrect:

http://mysite.com/http://mysite.com/path/to/dir/myfile.pdf

For those sorts of links to work, I need to set remove_script_host to true and relative_urls to true, but that then breaks other sorts of links. :(

Has anyone figured out a way to have both situations work properly?