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Hmm. I'd try rendering a movie with a picture that is exactly 16:9 and see what happens.
Like said before, its probably youtubes end. I know back a while ago you rendered at like... 1078p or something for the best quality. I had some issues where my videos came out extremely small inside the youtube frame even though its 720p/1080p, but youtube auto adjusted them.
I'm 90% certain that the problem is on Youtube's end, because I have the original videos saved and I can watch them with every programme I have without any issues.
I'm sure there's a way around it though, some channels upload hundreds of videos like this and they work fine.
Will be streaming again in a minutes time.
www.justin.tv/caumen