Here is a sample of how I set up the export.
http://www.platinumproductionz.com/images/pp_full_dialog.jpg
Here is a close-up of the specific sections you should pay attention to.
http://www.platinumproductionz.com/images/pp_bd_sequence_settings.jpg
Use the Export Foramt "MPEG2-DVD" or "MPEG2 Blu-ray", depending on which disk format you are burning. These Export types will not require transcoding in Encore.
(The 'Match Sequence Settings' check box is no longer checked because I modified the preset for max render quality, frame blending, etc.)
If you are creating a Dolby .ac3 file and it still plays stereo, then you are likely not using the "Surcode for Dolby Ditital" preset.