[Jon Miller]

One thing I realized – somewhat unrelated – is that if I had one of the Clone brush strokes selected in the timeline panel, making a new clone stamp brush stroke in the layer panel replace the selected stroke.

Work around I implemented: Quiting and relaunching After Effects. I found that what was being shown in the Layer panel was what ultimately would render in the composition panel. After quiting and relaunching the composition panel would correctly show what I had been seeing in the layer panel.

@Chris V – Did you find it was really an issue with the mp4 vs mov containers and not the codec? I haven’t been having any other issues with the footage for this project (all XAVC mp4s)