What Kevin fount is not my case. For me GNOME does not remember
programs. I have added it manually to Startup Applications. Works fine
for other programs, yet aMule disappears when minimized, somehow. It
does not disappear if opened by hand, i.e. without autostart enabled.

I have also checked that aMule is working and responding while being
hidden. I terminates nicely when I tell it to End through System
Monitor.

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Amule completely disappears when auto-started iconized
https://bugs.launchpad.net/bugs/93602
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