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videoWriter videoReader disorts file on linux

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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

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