There appears to be an issue with the new GTK in applications such as Eclipse that try to ignore the standard GTK structure, and have their own attempts at "magic" to improve the look. When GTK was upgraded in Karmic, this caused these magic tricks to stop working, breaking a lot of applications. Specifically whenever I would hit "Apply" or "Ok" in a dialog box, the button would depress, but would never trigger an action.
The quick fix is to change the way the application is called. For me, this involved going into the menu editor (right click on the launcher in your panel), and finding the application. I then found the "Command String" that looks like /path/to/eclipse and changed it to:
What this does is to tell the application's GTK framework to use native windows instead of the "magic" positioning and functionality that it used to rely on.