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.
Quick rant… if you, like me, use Ubuntu Hardy Heron or some other Linux distribution with SCIM enabled, and for some reason can’t use the ctrl+space auto-completion feature of Eclipse, check your SCIM key settings. In Hardy Heron SCIM gets input before other applications, like Eclipse, and ctrl+space is captured by SCIM and not send on to Eclipse. To get rid of that, simply delete that combination.
I don’t know why SCIM got enabled in the first place, but it’s pretty annoying. I know it makes you able to write Chinese characters ect. on the fly, but I don’t really need that! At first it had a bloody obnoxious input window pop-up all the time, but that’s easy to disable. For some reason the SCIM status icon in the panel can’t be removed. It has an exit option, but choosing exit only closes the program for a split second, after which it simply starts again. My best advice is simply to delete all keyboad shortcuts.