This bug is still happening in Xubuntu 13.10 64-bit.

** Package changed: libwnck (Ubuntu) => xfce4-panel (Ubuntu)

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https://bugs.launchpad.net/bugs/1192688

Title:
  MATLAB's Java windows disappear from the taskbar

Status in “xfce4-panel” package in Ubuntu:
  New

Bug description:
  I have seen past bug reports on this issue however it seems to have
  gone stale since 10.04. My machine is running Xubuntu 13.04 64-bit and
  the problem is with MATLAB R2011a Student Version.

  Randomly MATLAB's windows will disappear from the taskbar and the only
  way to access them is using ALT+TAB.

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