Yes, since the newest release of Rivatuner (2.0.1 I think, from memory) the settings stick after reboot.
I use Rivatuner to set my clocks and then ATI Tool to monitor/log my GPU temperature to a text file (NV driver monitor causes an annoying flash when it updates which I see in games when it's open in the background).
ATI Tool is also useful for looking for artifacts while ramping up your core/memory clocks. You can then use Rivatuner to set it when you are happy.
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