Blocking artifacts in H.264 decoded video

Hi,
I want help regarding a very strange problem I have been facing for the last few days. We all know that Microsoft has launched an H.264 decoder in windows 7. I am trying to use it in the following configuration.
[Camera]->[ffdshow video encoder]->[Microsoft DTV-DVD Video Decoder]->[VMR 9]
I am using GraphEdit to build the above graph. The graph works perfectly fine when I use the GraphEdit. However when I build the same graph using my own program, I get blocking artifacts in the decoded video. I have verified that the media types on connected pins are the same in both cases.
Can you please help me locate what I might be doing wrong here?
Regards
Abbas