Problem when HD movie (Final Cut Pro edited) viewed at smaller sizes on youtube

Does anyone else get occasional lines during motion (not interlacing) and motion jerks with their HD video when it is viewed in anything other than Full Size HD?
I am having this problem and it's driving me crazy trying to figure out where the problem is. Original footage was shot on an HD JVC Camera 1920 x 1080/50p AVCHD. Final Cut Pro converts it to 29.97 Apple ProRes 422 with Field Dominance: Upper (Odd).
Please refer to the attached file to see the compression settings I used in MPEG Streamclip. I found that I saw a lot of jumpyness before seting the data rate at 15000 kbps. There is still slight "lag" on panning shots, but watching the converted file on my computer and in Full HD on youtube (at full size) it is acceptable.
Is this a problem with youtube or with my conversion process? I have heard that AVCHD cameras have caused similar problems for others. Has anyone found a solution?
Thanks,
Spark

Here's an example of a file (.MTS) converted to H264 for youtube then uploaded with horrible panning problems:
http://youtu.be/hD8UnT_fv1s
And here's the piece I made which works perfectly fine when fully loaded and played full size in HD mode, but has glitches at any other size/ quality when played:
http://www.youtube.com/watch?v=4VHByjcs-n8&list=UUSCZm618F5deYQzcZLiw-vg&index=1 &feature=plcp
At around 0.51m, 1.20m and 2.08m motion lines/ glitches are most noticeable. Seems to happen mostly during panning/ movement shots.

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