I've had this problem when opening too many files at once. One of things that's great about jedit is the infinite divisibility of the editor window. I used to be able to open 15 separate windows. By reverting back 5.4 the problem exists but goes away if I close a file. In 5.5 & 5.6 the app needs to closed and reopened.
I'll add that the syslog shows: 2025-03-19T09:20:44.968807-07:00 INF-DEREK-LINUX jedit.desktop[34674]: Warning: $JAVA_HOME environment variable not set! Consider setting it. 2025-03-19T09:20:44.968886-07:00 INF-DEREK-LINUX jedit.desktop[34674]: Attempting to locate java... 2025-03-19T09:20:44.969225-07:00 INF-DEREK-LINUX jedit.desktop[34674]: Found a virtual machine at: /usr/bin/java... But BASH shows: $ echo $JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64
FTP plugin not working