[cwsand]

I'm not sure about the limitations of MPEG Streamclip, but my suggestion would be to find a better workflow - i.e. don't use Pro Tools as your primary video editor. I prefer to use video editing software to edit the video, then mix using Pro Tools. It's possible to use a single program for both, but most programs seem to focus on either video or audio and have suffering features on the other. But if all you're doing are straight cuts, I would think any decent video editing software would be able to edit the video and audio together and export a working file.