I have noticed this happen with other applications, too, ie the unity
launcher somehow loses track of the application so it no longer appears
in the launcher, but I don't know what causes it.

When it happens, does ~/.xsession-errors contain any useful information?

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https://bugs.launchpad.net/bugs/1001973

Title:
  netbeans icon does not show in unity launcher after starting and
  stopping netbeans a few times

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