Is it possible that the Jetty stop call is not logged in the *.log files?
I would be surprised (even more if there’s no request to the stop port). Just run basexhttp and basexhttp and check out the result:
16:49:45.431 SERVER admin OK HTTP Server was started (port: 80). 16:49:57.003 SERVER admin OK HTTP Server was stopped (port: 80).
Does the problem persist with RESTXQ, WebSocket, and WebDAV removed?
If you manage to create an environment in which you can also disable the BaseX REST service, and if Jetty goes down as well, it may be a problem that doesn’t relate to BaseX.