Timewarp effect in Ae CS6 causing footage to flash (some frames darker than those on either side)

Question

I have a clip sent from Pr CS6 to Ae CS6 that had some time remapping applied to speed up a portion of the clip. Although the dynamic link didn't work as expected, moving the in/out points of my clip from Pr in Ae, so that the footage in Ae was wrong, I was able to work around that by manually adjusting the footage in Ae to match what I started with in Pr (so much for dynamic link). That's not the worst of it, however. I sent this clip to Ae in order to add some motion blur to the newly faster footage to remove the strobing, using the timewarp effect. There is something funky going on when rendered, and it is different each time it is rendered. This is true in Ae AND in the clip that appears back in Pr. Sometimes it is perfect, but others some frames get darker, as if they are 2-3 stops darker, but only individual frames, and the placement is rather random between renders. I've checked the original clip in Ae, as well as the first comp of the original clip (2 of 3 pieces created in the project by dynamic link), and neither show these artifacts. Only the final comp, which has the timewarp effect on it to add motion blur, has this artifact, even in Ae. So, it must be related to the timewarp effect.
I've added 3 consecutive frames of one instance so you can see what I mean. Check out the middle frame.
When played back at full speed, this produces a very noticeable and annoying flashing. The last render I did had 5-6 of these weird frames. Any ideas on what could be causing this?
Thanks,
Shane

Answer 1

you have written a lot, but said very little. Rather than vague descriptions of the blue sky, exact info about framerates, exact settings, render settings, system info and so on would be much more useful. The answer probably is that either your footage is interlaced or you are using crooked values for your Timewarp, resulting in adjacent semi-transparent frames.
Mylenium