I believe that the pastebin is now completely working. Sub-directory support is in place, the favicon works in sub-directories. Geshi highlighter has been updated to the latest revision of subversion plus a minor fix from me to the mirc highlighter that was having problems with strings. I think most bugs have been squashed. Thanks for the endurance and testing of dark!
Get the latest most stable version of the Pastebin here.
Testing.