I am running Ubuntu 12.04 LTS 64 bit version and have been experiencing the 
same issue.
It seems that I can never input keyboard strokes and/or mouse clicks in Unity. 
In cinnamon (which I have installed as an additional DE) it sometimes is 
possible but also in this environment it does fail every now and then.

$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04.1 LTS"

$ aptitude show firefox
Package: firefox                         
State: installed
Automatically installed: no
Version: 15.0+build1-0ubuntu0.12.04.1

I have installed oracle sun java from the wepupd8 ppa (as described here: 
http://www.webupd8.org/2012/01/install-oracle-java-jdk-7-in-ubuntu-via.html) 
and my java version is:
$ java -version
java version "1.7.0_07"
Java(TM) SE Runtime Environment (build 1.7.0_07-b10)
Java HotSpot(TM) 64-Bit Server VM (build 23.3-b01, mixed mode)

If more information is required, please let me know.

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https://bugs.launchpad.net/bugs/111000

Title:
  Keyboard doesn't work within a java applet (Sun Secure Global Destop)

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