Bug while rendering with alpha channel
After Roto Brushing a selection on a previously roto-brushed video file, After Effects seems to have parts of the picture missing while rendering. This seems to happen with both After Effects and Media Encoder
The image below shows the preview of the first frame within After Effects on the left and within Media Encoder on the right.
I have been using the Roto Brush tool to designate the different layers and on my previous attempts the file rendered very accurately.
In attempts to solve this I have added additional Refine Edge strokes which have helped on the first frame, but there is no obvious sign where it is needed, meaning I would need to check every frame of the rendered file to see what parts are missing. See below. 
Any help would be appreciated, and yes I need to get a green screen.