Make sure you have the latest update installed and do not use Shadow/highlight in auto mode.
Auto mode can cause flickering.
Thanks Ann, I have the latest updates installed and I never use auto mode as I like to have full control of my image from the camera all the way to the final export. That's why I thought it was really strange that I had flickering. I have the full creative suite (now in CS6) and I have always had complete confidence in all my Adobe products, so I automatically assume its something I'm doing wrong when I don't get what I'm expecting from them. I wonder if anyone else in the community has experienced this. The only way I could remedy it was by taking the Shadow/Highlights effects off of the clips (which were had minor manipulations in that effect) and re-exported with good results. If I saw it in preview I would totally understand as I know how much strain it puts on the resources in order to render out a preview, but after it's gone through encode I would assume it should be all fine.
Thanks for your help.
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I have just installed PPro 6.0 and am finding the same flicker only in encode when a title ends while the clip below has sharpness effect. Take away sharpness, and the flicker disappears in the encode. This sucks.