Create a file in your home folder (or wherever you want) called eclipsefix.sh – open it and add the following lines:

export GDK_NATIVE_WINDOWS=true
/opt/eclipse/eclipse

then

chmod +x ~/eclipsefix.sh

got this from

http://mou.me.uk/2009/10/31/fixing-eclipse-in-ubuntu-9-10-karmic-koala/