I've installed a clean Karmic Koala amd64. 
No any JDK installed from synaptic.
I've downloaded the JDK from Java.com website and installed it.
I've downloaded SpringSource Tool Suite (Eclipse for Spring) and installed it.
added the following lines to ~/.bashrc


export JAVA_HOME=~/dev/jre1.6.0_17
export PATH=$PATH:$JAVA_HOME/bin
export GDK_NATIVE_WINDOWS=true

No problem to install new Software.
Then I've run the updates manager, installed all the updates and reboot the 
system and haven't found any problem to install new software from eclipse.
So, you can try to install a clean Ubuntu Karmic with no JDK from repositories, 
and download the jdk from Java.com and eclipse from eclipse.org

-- 
Eclipse crashes on Help -> Install New Software... -> Anything Done Here
https://bugs.launchpad.net/bugs/483882
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