I run into this problem a lot, the search dialog appears to be missing because it has opened far off screen. Resetting the search.x in the ~/.jedit/properties file to a low value should restore the dialog to a usable position.

The problem can be easily avoided by mapping the ctrl-F shortcut to a macro that resets the search dialog position before opening it (see below.) The dialog is not repositioned if already displayed.

/*
* Centered_Search_Dialog
* Centers and opens a search dialog
*
* Remap keyboard shortcut ctrl-f to this macro to always open the search dialog
* in the center of the current window. If the search dialog is already open,
* do not reposition.
*
* The selected text is always set as the initial search value.
*/
SearchDialog searchDialog = SearchDialog.getSearchDialog(view);
if(!searchDialog.isVisible()){
searchDialog.setLocation(view.getX()+view.getWidth()/2-searchDialog.getWidth()/2,view.getY()+view.getHeight()/2-searchDialog.getHeight()/2);
}
SearchDialog.showSearchDialog(view,textArea.getSelectedText(),SearchDialog.CURRENT_BUFFER);

I seemed to have solved this problem by switching off all the Java experimental options in Utilities->Global Options..., Appearance. We recently loaded a new Java version here with which those options apparently do not work.