I have also had the issue of struggling to render 5.1 audio from Cinelerra and have it come out in the correct channels. I'm sorry to say that I don't have a solution (being decidedly an end user and not particularly confident in understanding what's going wrong), so if anyone else has an actual solution rather than this rather convoluted workaround, please let me know. However, I do have a workaround.
Basically I render each audio stream separately as a mono channel .wav file (to do this, make sure you temporarily change your project settings so that there is only a single audio track, then ensure only the appropriate audio channel is set to play before rendering the audio). I then use sox to create