Looks like this bug hasn’t been fixed all together, the rear channels on a 5.1 encoded ac3 avi file are still being swapped around, the front channels are correct now though.
I suggest you download this little Tech Support Tool Reporter:
Fill it up, and send it to VSO Tech Support.
I know VSO are about to re-write the AC3 Decoder to fix several out of sync issues with AC3 Audio Streams.
It might be a good time to fix that one too