Looks like you have some Chroma values below 7.5 IRE, which may result in those green artefacts you got while rendering in Software Mode. Try Video Limiter effect with Signal Min set to 0.00%.
Meanwhile, I downloaded your YouTube file and found out that you also have a lot of overbrights throughout the video. Sometimes way above 120 IRE. Maybe some cumulative effect takes place on encoding, which results in errors in colour values calculation and hence those sudden black holes you're experiencing in 1:22:16. So, you may probably want to revise your approach to colour correction.