When jEdit 4.3.2 has been installed via Ubuntu package management, a shell script is used to invoke jEdit which differs from the one in the Java-based installer. I'm not sure that all the differences are intended:
1. Sun Java is used as the latest alternative, even when it is configured as default alternative.
This seems not to be in accordance to the recommendation at http://www.jedit.org/index.php?page=compatibility
2. The command line options "-background" and "-reuseview" are not used.
While each of them is a matter of taste, at least "-reuseview" should be used by default, I think. In general users are irritated about one jEdit view per each opened file.