theora: 4:4:4 video encoding is corrupted.
I'm filing this under 'libtheora', but it might be a problem with encoder_example. Please change the component if this is the case.
Y4M files in 4:4:4 colorspace generate Theora videos with what looks like a scaled and offset chroma plane. These files look the same when decoded with libtheora 1.0 (via mplayer) or with player_example from libtheora 1.1.1.
I'm attaching the source Y4M file (in 4:4:4 colorspace), the generated OGV, and screenshots of the Y4M video and the resultant OGV.