Does your jEdit file editor show you “Connect to FTP Server” window every-time you start it? And then if you cancel it and then try to load your bookmarks window or try to connect to a FTP connection through FTP plugin window it does show you I/O (input/output) error message?
This usually happen when you have selected a settings which says “Restore previously open files on startup” in Global Settings and then you exit the jEdit while being connected to some remote FTP connection. Next time when you start jEdit it tries to load the remote files by asking your confirmation. I think this is a bug (may be.. i am using it on Ubuntu 12.04) which causes jEdit to show I/O errors even if you cancel the FTP connection attempt window. And sometime it becomes frustrating when you have to do some very quick task on your local files and a slow connection may add to your frustration in this case.
To avoid this you may want to turn off this settings by visiting Utilities > Global Options > General and uncheck the “Restore previously open files on startup” option.
Just a quick note.