Part of Output movie Jittery

Hello. I am new to PI 3.

I am taking a movie that i have rendered out in After Effects 7.0 (settings same as i've always used) that looks perfect. Setting it as my background image in PI with separate fields "off."
After applying emitters and whatnot, i have tried outputting as Quicktime Movies with numerous different settings, and as a Targa sequence, but my end result is always a clip that has some jitters. Any ideas what i may be doing wrong off the bat?

Let me know if anyone would like more specific details.

Thanks for any help you can provide.

Bryon