How did you create this AppDir? It is missing a lot of things:
1. The AppRun executable (this is what gets executed)
2. The binaries in usr/ need to be patched so that they have no hardcoded "/usr" in them
3. Exec=gksu /usr/sbin/gparted in the .desktop file won't work
4. The libraries in usr/lib are missing
If AppImageAssistant created this, then it didn't run all the way through to the end... probably because this app requires root rights.
I have corrected the above and was able to create an AppImage just fine.
The AppImage must be run as root (e.g., with "sudo" from the command line)!
So I'd say AppDirAssistant *is* working properly
PS: If you want to compare, unpack with AppImageExtract (it will extract the AppImage to $HOME/Desktop): http://www.mediafire.com/?xkr64x1nn0rntlz