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hardware encoding and multi frame rendering are basically just hacks- they don't work everywhere, and they cause system instability. AE was made for single core machines with no GPU's and a couple gigs of RAM at most. it was then hacked to use a little GPU, throw everything in RAM instead of disk, and its processes were naively duplicated one per frame for each core. Now, you hack that gpu hack to get it on a SOC style chip like the new MAC's with a new GPU archetecture, with RAM and VRAM being the same thing and all on the same massive CPU chip... there's issues there.
I can turn off hardware acceleration, and the flickering goes away.
you seem to have found a workaround, and given the instability, I do that too, even with an nvidia 1070 and intel 6700k. Adobe likes to push their new features super hard, but it seems their new features and optimizations aren't very robust or performant. Even with all the "optimizations" as of late, AE still runs 22% slower with all of them than CS6 from 2012. Default settings are what they want you to use, and try out, and test for them, not what works or what you're here for. The devs are generally more interested in being important than useful, which is an important distinction to make.
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