Hi jfraze. I tried the uploaded original video in the latest v9.09 Mac release and the resulting mp4 files were good. Tried multiple times with lossless mode enabled and disabled. Does it only happen in mp4 format? How about using mov, flv, or avi? Please also try using H265 format in mp4 or mov format.
What is the macOS version and model of your Mac? What is its GPU?