I have a project with a mix of 1440x1080 tape at 24fps and AVCHD at 1920x1080 at 24fps. When I render, I get green lines across the AVCHD shots. I have tried creating sequences in 1280, 1440, and 1920 and they all play fine in the timeline. But they all render with the green lines, whether I choose FLV/4V, H.264 1280, H.264 1920, or match sequence from a 1440 sequence.
That's a new one for me.
I'd check to see if you're using the most updated graphics drivers for your graphic card and then do basic maintanence on Premiere Pro http://blogs.adobe.com/genesisproject/2011/02/premiere-pro-cs5-maintenance-two-great-tips. html