Can't replicate it in Sandbox, as there doesn't appear to be a way to setup dual monitors in sandbox, and this only happens on a second screen. However as I mentioned, I recently reformatted, about 6 weeks ago, and on a fresh install of the OS where Start11 was one of the first things installed it still happened.
For a moment there I thought it might have been a conflict with Notepad++ as that was often starting the flickering at the same time it was running, however proved that wrong as it seems to just happen regardless of what's running.. Any other ideas on testing?