So in the dolby AC3 custom setup if you select a 2/0 channel format you then get the choice in the bitstream tab of "dolby surround encoded".
Does this create a Dolby Pro Logic encoded 2 channel AC3 file?  This is from a surround project.  
Or, is the only way to get something like that as described in this thread:
[link = 
http://www.sonycreativesoftware.com/forums/ShowMessage.asp?ForumID=19&MessageID=653559]