videoWriter videoReader disorts file on linux

Matlab R2011a on Ubuntu with latest version of gstreamer 0.10

Basically my code uses videoReader to read in video frames then pads alternate lines of the video with a few pixels to improve the interlacing. I then write the new video out with videoWriter. The code seems to work perfectly under Windows however when I run it on my linux machine the output file is distorted. I have uploaded examples of input http://dl.dropbox.com/u/91060467/input.avi and output http://dl.dropbox.com/u/91060467/output.avi videos to dropbox. Code is reproduced below.

Thanks

if true
function paddingTest(filename,iPad)
  [pathstr, name, ext] = fileparts(filename);
  mov=VideoReader([pathstr filesep name ext]);
  nFrames=mov.NumberOfFrames;
  vidHeight=mov.Height;
  vidWidth=mov.Width;

    frame_in(vidHeight,vidWidth,3)=uint8(0);
    frame_out(mov.Height,mov.Width+iPad,3)=uint8(0);
    movie_out(1:mov.NumberOfFrames) = struct('cdata', frame_out,'colormap', []);

    for idx_frame=1:mov.NumberOfFrames
        frame_in=read(mov,idx_frame);
        frame_out(1:2:vidHeight,:,:)=[frame_in(1:2:vidHeight,:,:) uint8(zeros(vidHeight/2,iPad,3))];
        frame_out(2:2:vidHeight,:,:)=[uint8(zeros(vidHeight/2,iPad,3)) frame_in(2:2:vidHeight,:,:)];
        movie_out(idx_frame).cdata=frame_out;
    end

    writerObj=VideoWriter([pathstr filesep name '_new' ext],'Uncompressed AVI');
    open(writerObj);
    writeVideo(writerObj,movie_out);
    close(writerObj);
  end