I ran into this issue while installing the Google App Engine... a quick description of the problem is that some buttons in Eclipse were not responding (doing nothing) after I upgraded to Karmic Koala, after checking the log file, network connection settings and some other things that didn't work I decided to ask the oracle (Google) about it and after a while I found a simple and quick solution here.
Just create an executable file with the following content:
#!/bin/sh
export GDK_NATIVE_WINDOWS=1
/opt/eclipse-3.5/eclipse
Now back to coding ;)
