> It seems to just silently fail and nothing happens.

Would you check ps to make sure it’s not running without a window, e.g., run: 
ps auxwww | grep mged

> in the desktop entry below; changing Terminal=true; mged will start.

Yes, that’s to be expected.  That’s the terminal detection I mentioned.  The 
thing is that it should also be running when there’s not a terminal, but 
obviously isn’t working as intended.  I suspect there’s input on stdin and it 
thinks it’s in command mode (where it runs one command and exits). 

> here's the contents of my .desktop file;

Thanks, what OS is this on?

Cheers!
Sean



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