Is question 4 ("aMule starts but is never shown but works fine. What's going on?") still relevant?
I'm referring to the first paragraph: "This commonly happens when you set the type of systray integration, in Preferences -> General -> Misc Options, to Minimize to trayicon which starts aMule minimized."
There's no longer a systray integration in Preferences -> General -> Misc Options. Only two options: "Minimize to tray" and "Start Minimized"