When the launcher detects that an update is available, and the user agrees to update (by means of the GUI prompt), then after downloading and installing the upgrade the game quits. Attempts to start it by invoking mule.sh (possibly by means of GUI integration, i.e. a M.U.L.E. starter on your Gnome panel) will fail since that file is no longer executable (but it was before the upggrade).
Possible fixes:
- Either mark mule.sh executable before wrapping it in the updater archive and use tar.gz archives which can retain the executable flag, or...
- have the updater script run chmod +x on mule.sh after unpacking on Linux.