I suspect the flickering is there to stay. The AMOLED screen has a zillion LEDs to turn on/off for the three primary colors that are used for each pixel, Red, Green and Blue.
IF the CPU is busy doing other stuff, then the processor time is shared between all of the different things. It may be weighted in favor of the screen, but not totally, so the flicker coming and going is normal. That some are experiencing worse flicker after Denim suggests that time share priority to each CPU cycle has been changed.
To test this theory you could turn off all background tasks that you can. Then disconnect wifi and turn off radio (if possible) and then let it sit for a few minutes to let the CPU load (if any) settle down. Then, test for scrolling jitter and flicker where the CPU has little other stuff to share it's time with.
Just look at the PPI (440) of the AMOLED versus the LED (around 290-330) screens and understand the work load that has been thrust upon the AMOLED. Little wonder that the next phones from msoft are going to have 800MHz processors, maybe even 64-Bit, the 200 and 400 are not cutting it with AMOLD. Also note that 64-Bit will not make much difference to the screen performance though, but the 800MHz will.