We've hit a problem with the normal situation where we're running eXist listening on a different domain from localhost. To summarize:

If eXist is running on the default localhost:8080, I can use startup.sh and shutdown.sh to start and stop it.

If it's listening instead on another ip name, I can still start it with startup.sh, but I can't stop it with shutdown.sh or with start.jar directly. I get:

ERROR: Failed to create input stream: Unexpected end of file from server
CAUSE: Failed to create input stream: Unexpected end of file from server

Disowning the process in the terminal where it was started makes no difference. Supplying credentials also makes no difference. Waiting to see if anyone on the eXist list has any ideas.