kherio,
I've been doing some test this evening after reading your post. It has nothing to do with being super-user or not. The problem is (ir that's what it seems to me) that you had already an ~/.aMule directory created, but no ~/.eMule file. When aMule sees there's an ~/.aMule directory, ti doesn't check for an ~/.eMule file. I've already added that to the Known Bugs list.
You can walkaround it by renameing your ~/.aMule file, opening aMule (now an ~.eMule file will be created), cloeseing aMule, removeing your new ~/.aMule directory and renameing yor old ~/.aMule directory back into it's original name (that is, ~/.aMule ;-) )
So, just type:
#!/bin/sh
mv ~/.aMule ~/.aTemp
amule
# (Wait for amule to be loaded and then close it as normally)
rm -r ~/.aMule
mv ~/.aTemp ~/.aTemp
I hope that helped. Please keep informing so that we can make aMule v2.0.0 a bug-free release ;-)
Greetings and thanx!