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I think the simplest way of finding out what is causing it is to simply take the marathon promo video, then reencode it, and removing option after option until the problem goes away.
I don't have the time myself, though.
Edit history:
Aktan: 2011-02-12 08:41:13 am
To me, you should send anything to YT with as high quality as possible, since YT transcodes anyway.  If you have the bandwidth, I would send lossless H.264, or else send some constant quant and turn off b-frames.
I agree, though I don't know if YT supports H264 lossless.
Oh, it does.  Like the example I gave.  That was lossless H.264.
The Anomaly
I also had this problem with my youtube uploads. After extracting the audio and video tracks with yamb and remuxing them into .mkv with megui I got it to work.
Well after doing a ton of testing, I found out the problem was header removal compression. Here is some information about it:

http://www.bunkus.org/videotools/mkvtoolnix/faq.html#header_removal_compression

Apparently YouTube demuxer doesn't support it, which is why the video is gray.
Edit history:
ballofsnow: 2011-04-10 10:00:44 am
ballofsnow: 2011-04-10 09:55:22 am
Posting test results on unreleased anri 3.3. x264 version r1924.

Same video as before.

Source video is 720p, 30 fps, 20 second duration, with statid, total 30 seconds:
LQ
MQ
HQ * 48 seconds!
IQ * 48 seconds!
XQ * 48 seconds!

LQ:
Writing library                  : x264 core 114 r1924 08d04a4
Encoding settings                : cabac=1 / ref=16 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=10 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=24 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=12 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / constrained_intra=0 / bframes=8 / b_pyramid=0 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=60 / rc=2pass / mbtree=1 / bitrate=128 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00

MQ:
Writing library                  : x264 core 114 r1924 08d04a4
Encoding settings                : cabac=0 / ref=1 / deblock=1:0:0 / analyse=0x1:0x111 / me=umh / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=0 / me_range=16 / chroma_me=1 / trellis=0 / 8x8dct=0 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=12 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / constrained_intra=0 / bframes=0 / weightp=0 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=40 / rc=2pass / mbtree=1 / bitrate=512 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / vbv_maxrate=768 / vbv_bufsize=768 / nal_hrd=none / ip_ratio=1.40 / aq=1:1.00

HQ:
Writing library                  : x264 core 114 r1924 08d04a4
Encoding settings                : cabac=1 / ref=16 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=10 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=24 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=12 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / constrained_intra=0 / bframes=8 / b_pyramid=0 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=60 / rc=2pass / mbtree=1 / bitrate=2048 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00

IQ:
Writing library                  : x264 core 114 r1924 08d04a4
Encoding settings                : cabac=1 / ref=16 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=10 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=24 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=12 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / constrained_intra=0 / bframes=8 / b_pyramid=0 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=60 / rc=2pass / mbtree=1 / bitrate=5000 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00

XQ:
Writing library                  : x264 core 114 r1924 08d04a4
Encoding settings                : cabac=1 / ref=16 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=10 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=24 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=12 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / constrained_intra=0 / bframes=8 / b_pyramid=0 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=60 / rc=crf / mbtree=1 / crf=17.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / ip_ratio=1.40 / aq=1:1.00


It's got that grey screen effect at the beginning of LQ/HQ/IQ/XQ, not on MQ though which uses different settings.