Just found this post which deals with the exact same problem that I have been fighting with…
After upgrading to Ubuntu 9.10 (Karmic Koala) some buttons no longer work in Eclipse 3.5. Clicking has no effect but keyboard shortcuts still work.
Create a script to start eclipse with the following export…
… and remember to change the path to where your eclipse is located.
Check http://www.norio.be/blog/2009/10/problems-eclipse-buttons-ubuntu-910 for a little more background on the problem.