You should update your BIOS to the newest ATI version. That fixed the flickers for me and why your there you could change the BIOS fan profile so you wouldn't need to use additional software or profiles to mess with the fans. You can change the fan profile with Radeon Bios Editor.
According to Unwinder the developer of Afterburner there is a Performance hit when using Afterburner to control the fan speeds on ATI cards. So its better to let the BIOS handle it or set static speeds.
I have no idea what you are talking about to be honest. If I set it in bios then they would always be at the speed I set in the bios. That defeats the whole purpose of what I was trying to do.
I actually reinstalled the 10.3 driver and now I am not having the flickering issue.
And can you provide facts, proof of him saying that and or a source.