hi Alessio,

from the link you posted:
  
http://askubuntu.com/questions/36434/how-can-i-remove-duplicate-icons-for-launched-java-programs-in-the-launcher

# run this, then select the freeplane window:
$ xprop | grep WM_CLASS

# on my system:
WM_CLASS(STRING) = "sun-awt-X11-XFramePeer", "java-lang-Thread"

=> have you tried to modify: 
 
  /usr/share/applications/freeplane.desktop

to add a line:

StartupWMClass=sun-awt-X11-XFramePeer
or
StartupWMClass=java-lang-Thread

and logout+login?

Best Regards!
-- 
Felix Natter

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