The reason for the weirdness according to how you start it is that when you run it from a terminal you are already in your server folder, so it can find the server.
When you just run it from the "file browser" (nautilus?) you are running from your ~/.desktop, so it can't find the server or the other scripts.
On my machine, I always run them like this:
Code:
ssh paranoia xterm -e ./starteqemu
and
Code:
ssh paranoia xterm -e ./stopeqemu
where paranoia is my server, and the script starteqemu is in my home directory on paranoia and contains
Code:
#!/bin/bash
cd eqemu/server
./start
read $fish
stopeqemu is similar
The read command waits for a carriage return, so I see error messages if something goes awry during start-up.
I've never tried to run the server by clicking on things.