A colleague came to me today and said he couldn't press the 'Finish' button when he was trying to upgrade the eclipse plugin inside Help->Check for Updates. It rings my bell and I did solve the problem when I upgrade my Eclipse to 3.5 a while ago. At that time the problem was around the Search dialog button is unresponsive when I click it. And I can only press 'Enter' in order to issue the search action. I guess it's the same issue and I think it's good to blog it down here in case I forget the solution again.
To solve the problem, you have to set the following variable in your system before you run Eclipse:
export GDK_NATIVE_WINDOWS=true
Then you should be able to click the buttons again.
* System environments: MacOS 10.6.x and Ubuntu 9.x
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