Just sorted it!!
Go Apple menu to Control Panels, to Keyboard. Click Options. The Hot Keys checkbox should be ticked. Click to uncheck it, close the Control Panel, and your OS, Quark etc Fkeys should work as normal.
If you want to configure Hot Keys to open applications, games etc, check the Hot Keys box, but hold down the Options key when using your Fkeys, to do the normal stuff (cut, copy, paste, show/hide etc).
If only relationships were as simple...