Thanks Robert Niessner ! Yea, I'm starting to learn that's the case.
In case anyone finds this post looking for a solution, I think I've figured out a way to get 5.1 surround to export properly with Voukoder on CS6.
Basically, you want to fool CS6 into arranging your tracks in the standard layout of L+R+C+LFE+Ls+Rs. One way I've found to do that is to create your sequence with a 5.1 master audio and then have your audio tracks set to adaptive. In the audio mixer, you now need to have each track send its audio to the standard layout (which will conflict with premiere's layout, but when you export with Voukoder it'll be correct).
So have
all Front Left audio tracks output to 1
all Front Right audio tracks output to 2
all Front Center audio tracks output to 3 (this will make the audio come out of Left Surround channel on CS6, but again it'll come out of the correct Front Center channel when you export)
all LFE audio tracks output to 4 (audio will come out of Right Surround channel on CS6)
all Left Surround audio tracks output to 5 (audio will come out of Front Center channel on CS6)
all Right Surround audio tracks output to 6 (audio will come out of LFE channel on CS6)
And you're good to go! Of course, you can do all your editing in the regular CS6 layout or use Audition, then before you export rearrange the track outputs to the above layout.