Jamie,
I’m curious as to where exactly you are noticing the loss of quality.
What I’m noticing is in the first video some pixelation on the effect layer over the video in the into and in the second video some lines in the sky.
From my experience, I think those problems come from a low bitrate. When exporting for 1080p HD your bitrate should be 10,000 – 20,000 kbits/s.
My guess is that when YouTube converts your video, the lower bitrate starts to bring out the pixelation and lack of information in the sky, so I would try exporting with a high bitrate then uploading to YouTube and see how that looks.
Hope this helps. You may want to post your export settings also.
Morgan