After reading this I installed Lion with hopes that Lion would be the solution to this flickering. Unfortunately, after installing a Lion and switching to Better Battery Life, within seconds, there was flickering! The flickering was much worse than ever. A tear ran down my eye...
To everyone speculating that going back to Leopard would remedy the solution, from my experiences, don't bother. At least Leopard 10.5.6 onward. I got my MacBook Pro back in 2009, the one with the 2.66 GHz, and it came stock with 10.5.6. From the day one, running the 9400M, there has always been flickering. So far, I wouldn't be posting this if there has been a solution, none of the updates, both Leopard and Snow Leopard, has fixed or even eased the flickering while running the 9400M.
I do not think anyone pointed this out, but there is even flickering during the grey boot screen after turning on or restarting the Mac, before the OS loads. From that I think that this problem, this defect or bug, extends beyond the software and OS. It could be either the firmware or hardware.
Apple so far is either failing to respond or ignoring this problem. I bought Apple Care for my MacBook Pro, optimistic that they will be able to fix this problem within the three years after buying it. However, so far, they seemingly have done nothing, they could at least respond that they are working on the problem. Over the summer, on break from school, I plan to go to a Apple store and work this out. With the knowledge that sending it in for replacement of the logic board or screen doesn't fix the problem, I will keep doing that, just to show those seemingly ignorant "Geniuses" that won't fix the problem. After some number of "repairs" I will either demand a full refund or a replacement with a newer generation MacBook Pro.