Yep. I had the same problem, but the solution was simple.
You need to render it as if you didn't have the AC-3 Encoder. (i.e. render it as 48000 16-bit mono.)
It will automatically divided it into 6 streams and then you just import that into Vegas.
Then you need to assign each channel for each stream.
Each stream is labeled as "right" "left" etc. already.
Then you can render the music, and other sounds, with the AC-3 Encoder via Vegas.