Just a note:
After upgrading my Ubuntu machine to latest Ubuntu 12.04 LTS version my preferred code editor started to have issues. I opened it as normal and it showed me 3 FTP connection windows at once and after closing these windows when i tried to launch a FTP profile from bookmarks it didn’t work and kept saying the “Already running command error”. I thought i needed to re-install the jEdit (the upgrade actually re-stalled the latest release of jEdit while upgrading) and tried a re-install but it did not fix anything. Then i removed the FTP plugin of jEdit and re-installed it and hurray, it works!