I think I've finally figured it out why some icons are disappearing from
the launcher.

Another test case:
* Make sure you have no browser running
* Install Netbeans 7.2.1: prefer the JavaEE version
* If everything went fine, you should end up with a desktop shortcut. Run it.
* It should add two icons to the launcher: only the second one points to the 
real app, while the first is useless (this is very annoying by itself, but 
that's not the main point)
* Create a new web application: File -> New project -> Java Web -> Web 
Application
* Run the project: Run -> Run project

Supposing you already have Firefox locked to the launcher (and again, it
wasn't running before you started this test), surprise: Firefox starts,
but nowhere you can find its icon, neither at the launcher nor at the
alt+tab list. The only way you can focus Firefox again is using Super +
w.

Update: as if it wasn't odd enough... Turns out if I click the first
Netbeans icon (the useless one), Firefox shows up. So it seems that, at
least for a Unity point of view, the parent process (Netbeans) somewhat
"owns" the child process (Firefox).

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https://bugs.launchpad.net/bugs/995916

Title:
  No launcher icon or Alt+Tab entry for Gimp windows

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