Yes, I think its a bug from gnome, gnome hides xxx.desktop if it link to
a non-exist binary.

step of installing deb packages ->

1、dpkg decompresses /usr/share/applications/virtualbox.desktop to system
(System found out it links to /usr/bin/Virtualbox but it not exists, so
hide it)

2、dpkg decompresses /usr/bin/VirtualBox (till now, the like file
appears, but it is late..)

Thus, icon is not shown after installion, but by restarting gnome-panel,
it will come out.

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https://bugs.launchpad.net/bugs/1530555

Title:
  virtualbox icon isn't shown in menu from gnome-panel once virtualbox
  is installed from apt

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