I would advise dumping MPEGStreamclip and getting Compressor to do the encoding. I've been really happy with the H.264 encoding of Compressor 4. It's able to use all 8 cores of my MacPro. Very efficient and it doesn't have all the bugs of MPEGStreamclip.
Brad Wright is software engineer, so it may be difficult to understand what he is saying. He is always happy to explain his greater detail.