Some more info about this bug. I could reproduce it in several PCs.

In the case of ClipGrab (which was installed from its ppa: ppa:clipgrab-
team/ppa) sometimes, it has to be opened several times in order to see
the bug. When the bug is not present, it shows two icons in the launcher
briefly, and then one of the disappears, leaving only one.

For KeePassX, the bug is only present when the program is trying to open
a database on startup. It asks for the password, and the it closes the
password dialog and opens the main window. The icon disappears when the
password dialog closes and does not reappear when the main window opens.
If there is no database to open, and no password dialog appears at
start, the bug is not present.

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https://bugs.launchpad.net/bugs/1002874

Title:
  Some apps doesn't show in the launcher when opened

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