This is worth a try - it worked for me! I had the same problem with mysterious flickering on output from Premiere Pro. It looked perfect in PP while I was in the program itself just previewing it but always generated flickering when I rendered it. The work-flow is that you do all your work in Premiere like normal (including dynamic links to AE if needed). Once you are done, then close PP, open the file in AE and render your sequence in AE (you can hand it off to Media Encoder from AE).
OK, here are the steps:
1. Create your sequence in PP, preview it to make sure it is correct, but don't render it via PP
2. Close Premiere Pro
3. Open After Effects and Import the Premiere Pro file. From the pop-up window only select the sequence that you want to render. In AE, drag this sequence down to create a simple composition.
4. Render this composition from AE. You can hand it off to Adobe Media Encoder.
That's it! Hope it works for you. It definitely worked for me and solved this maddening problem with PP not being able to render effects, ultra key, and other special effect correctly without flickering. Just do all your work in PP (including dynamic links to AE), save the PP file, Import that file/sequence in AE and render this composition from AE. I also didn't notice any longer render time via AE verses PP.