Get rid of the "#Terminal 1200" line. It only works with the PE.
If that doesn't work try replacing it with: "#com /dev/ttys0" and see what happens.
The only thing that stops me getting the terminal window is when I don't have the download cable connected. You could have a look at /home/username/.LinAXEpad/axepad.ini to check the [Linux Target].
Try going to the folder containing LinAXEpad then right-click/"Open a terminal here". Type ./LinAXEpad then try to open the terminal window. You might get some usefull error messages.
You could put a "debug" command in your program to see if you get the debug window.