Problem with ffmpeg or the source?

[Shevek]

When I downloaded get_iplayer it installed version r25557 of ffmpeg.

A while back I noticed that this started to output an error during its
processing:

"brainfart cropping not supported, this could look slightly wrong ..."

(although the output would still be ok)

So on 6th Dec I started using later builds of ffmpeg downloaded from
http://ffmpeg.arrozcru.org/ and the error went away

However I noticed yesterday that there is an odd shift in the mp4 output.

In this example, the HD version of ep 7 of Simple Suppers (b00wqb9p).

As you can see from the grabs (linked below) there is a green and pink
strip across the top and a "shadow"

I have tried all of my downloaded versions of ffmpeg - r25895 (6/12)
through to r26041 (today) and they all output like this.

I have grabs from the original flv, the r25557 remux and the r26041 remux.

What can be causing this? Is it ffmpeg or is it a dodgy encode on the server?

I have re-downloaded the HD version and the vhigh version.

The vhigh version remuxed using r26041 is fine

Original HD flv: http://paje.ro/wp-content/uploads/2010/12/hd_flv.png

Remux HD using original ffmpeg:
http://paje.ro/wp-content/uploads/2010/12/hd_r25557.png

Remux HD using latest ffmpeg:
http://paje.ro/wp-content/uploads/2010/12/hd_r26041.png

Original vhigh flv: http://paje.ro/wp-content/uploads/2010/12/vhigh_flv.png

Remux vhigh using latest ffmpeg:
http://paje.ro/wp-content/uploads/2010/12/vhigh_r26041.png