I recently upgraded to Mac OSX Snow Leopard and was really sorry that I lost all the Eclipse function keys, as they are reassigned for the OS: Show Dashboard, brightness up/down, etc. Luckily I soon discovered this option in System Preferences for Keyboard:
Luckily it also work the other way around, so you can keep f4 to mean Dashboard, but use fn+f4 to do Show Hierarchy.
It was the same way in Leopard. Maybe you had changed the setting and after the upgrade it went back to Apples default.
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