Yeah, I’m sticking with Compressor from now on since it maintains the dual mono tracks. The downside is that Compressor takes a REALLY long time in comparison to MPEG Streamclip, and I typically have about 10 hours of footage to transcode at a time. But I shoot in some pretty noisy situations, so it’s important that I’m able to separate the lav from the shotgun.
If time is of the essence for you, I’d say just stick with what you’re doing as long as it’s working. Otherwise, you might want to switch to Compressor. I mean – I loved Streamclip until I realized it was turning my audio into stereo. It amazes me that a program like that wouldn’t even give you the option of maintaining the integrity of the audio tracks.