problem generating movies w. modern compression

I get skewed and striated movies when i use avifile with a custom compression (windows7). I can see that several people has had this problem on the newsgroup, but i have found no solutions.

I do the following:

set(gcf,'pos',[400 300 854 480])
aviobj = avifile('RCP45_inmcm4_r1i1p1.avi','fps',60,'compression','FFDS');
for ii=1:200
    plot(randn(100,1)) %... draw some stuff ...
    drawnow
    F = getframe(gcf);
    aviobj = addframe(aviobj,F)
end
aviobj = close(aviobj);

Regarding the FFDS compression: My last attempts has been using various settings in ffdshow-tryouts to no avail. http://ffdshow-tryout.sourceforge.net/

I would like to encode using a modern codec like h264 or webm (even mpeg2 would be nice.) So, any solution that tells how to do that would be great.