Hey Adobe, here's some more info: I have the same thing happening to me in PPro 6.0; in my encode (NOT in preview), when the title ends, the video with sharpness effect flickers. Kill the effect, and then encode, and the flicker is gone. I'm encoding an 1080p .mp4 at 24p from a 720x480 @ 29.97i sequence.
About to try sticking with an interlaced output from my interlaced sequence...