I've had a few similar reports in the past MSI Afterburner sometimes doesn't like too frequent clocking changes request. Can you try to put a delay between the clocking operations by going to the Options dialog, Mining Settings and add a few seconds to "Pause after applying clocking settings".

I can also announce that the development of native clocking via Awesome Miner has started. It's a bit too early to say how it will work out, but it looks promising and the plan is to let Awesome Miner do the clocking via the AMD and nVidia libraries/drivers without using external applications like MSI Afterburner. This will give Awesome Miner much more control of the clocking in the future.