This macro (based on preview javadoc macro) makes jedit hang:
runInSystemShell(view, "echo 'nothing.java:290: error: forced error' && sleep 1 && echo x");
It is based on linux sleep command, but one may rewrite it using another os commands. The clue is in outputting an error line, to be intercepted by ErrorList plugin, and after a while outputting another line. The deadlock comes from the fact that Console (indirectly through ErrorList) tries to send an EditBus message which waits until EDT thread is available. And EDT thread is blocked by the macro, which waits until Console finishes the command.
I use fresh trunk versions of jedit, Console, ErrorList on Linux. A relevant part of thread dump attached.