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0e1f616
(Get the code!)
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).