This is a problem I've had for a long time. I'm not entirely sure when it started, or if it ever worked properly. I am compteley sure I've never seen it on Windows though, only Linux.
This particular problem occurs when using the Meta-Insert -> Create getter/setter or Control-O (override method). Both of these pop up a dialogue window asking me for the fields to wrap, or methods to override. However, sometimes this window is not activated, so I can't select anything in it using the keyboard. Instead, I have to move my hand to the mouse to click in it to select it. It doesn't always do this though, which actually makes it even more annoying.
This happens both at home and at the office. Both of these machines run Fedora and GNOME. It's quite possible that it works with other window managers.
Has anyone else experienced this?