Black, flashing frames in render!

I have a big feature film I'm trying to export out and annoyingly a number of shots throughout the film have those annoying black frames strobing/flashing through them!
It is a pretty big project, 90minutes.  Some shots use warp stabilization, few shots in the timeline are linked to AE comps, and nearly every single shot has Colorista and MB looks effects on them, some also have addt'l color masks on them.
The last export took 4 days.  CUDA was on in Premiere, but MB looks had to have OpenGL turned off (due to issues with MB Looks otherwise).
I've tried to find similarities between the flashing shots (most do not flash, just some) but it seems pretty random...  Some shots with heavy color look fine, others dont.  Some shots with stabilizer look fine, others are flashing.  Same with AE shots.
When i export short, few second clips - it looks fine.  The problem happens when I export the whole film.  But I can't possibly play 'trial and error' when i have to wait 4 days for a complete render!
Please help!  This is really urgent.
I'm using Premiere CC with an Nvidia Quadro 2000 card.  All media files on external USB3.0 drives.
thanks,
Matt

Hi Jim Simon,
I was told that 1920x810 is the standard RED Wide format. So I wanted my 5d video to look the same as the RED wide.
"When a commercial widescreen movie is mastered for distribution on Blu-Ray disc, it's rendered at the full 1920-pixel width of the FHD format. Due to its wide aspect ratio, however, the movie's height covers only about 810 pixels of the 1080-pixel height of the screen, with upper and lower borders letterboxed. This 1920x810 frame is the native size of widescreen Blu-Ray video."
And also I really don't think that the sequence size would matter to render the project.

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