I have done some further experimenting and here is what I found:
First of all, the problem occurs only when using the surcode. In the case of the big CS6 project I was able to use the workaround of creating a 5.1 wav file then creating a new ac3 file from that.
With the reconfiguration of the Premiere audio tracks in CC, it seems that in order to properly transcode a 5.1 sequence with the Dolby Surcode, all audio clips in the sequence MUST be mono. Therefore any stereo source clips must be split into two mono clips and laid in on two tracks.
The dialogue tracks of my large converted projects are all mono, but I am assuming the problem is being caused by the stereo clips in the sequence.
For that existing project, I'm just going to continue using the workaround rather than reconfiguring the entire timeline.