Public bug reported:

Binary package hint: unity

Certain Java archive applications (applications ending with .jar) will
not dock correctly when a launcher is created (when a .desktop entry is
created and added to the launcher, pressing the .desktop entry will add
another icon to the launcher instead of the same original icon recognize
by it self the running application). There are only two examples that I
know, one of them is some kind of Portuguese dictionary-speller called
Lince and the other one is Minecraft which is more likely to be known by
some.

Here is my .desktop entry for my Lince application (the Minecraft one
should be similar)

[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Exec=java -jar /usr/local/Lince/Lince.jar
Name=Lince
Icon=/usr/local/Lince/icone_lince_32.png

jose@JARR-Laptop:~$ lsb_release -rd
Description:    Ubuntu 11.04
Release:        11.04

jose@JARR-Laptop:~$ apt-cache policy unity
unity:
  Installed: 3.8.12-0ubuntu1
  Candidate: 3.8.12-0ubuntu1
  Version table:
 *** 3.8.12-0ubuntu1 0
        500 http://archive.ubuntu.com/ubuntu/ natty-updates/main amd64 Packages
        100 /var/lib/dpkg/status
     3.8.10-0ubuntu2 0
        500 http://archive.ubuntu.com/ubuntu/ natty/main amd64 Packages

** Affects: unity (Ubuntu)
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/781442

Title:
  Certain Java applications won't be docked correctly in the Unity
  Launcher

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