I racked my brain out trying to find out what was causing this issue. Periodically, while switching from the editor to ftp and then to browser, upon switching back to the editor, the only item displayed would be the title bar. Dragging the window off screen and back did not force a refresh. It only caused the wavy line effect you get when dragging windows around and windows gets bogged down trying to keep up with a screen refresh.
Finally, I figured out what was going on and it is definitely a bug within the core of the editor. In the editor I have the registers as a dockable window and always visible as I am regularly copying and pasting a variety of code from multiple sources, using several registers at once. The problem only comes up when I switch to explorer and copy a file to paste into my ftp application. After copying the file, jEdit fails to update any of its buffers or windows until I select some text and copy it into the clipboard. (BTW--after the problem is fixed by selecting text, I still have to switch applications, or minimize-restore to trigger a repaint, but from then on it will work until I have to copy a file again.) I think this is due to the clipboard register always being present and displayed.
The error does not happen if the registers window is not visible, but if you click the button to display it while windows has a file in the clipboard, it has the same problem.