I see from the screen grab that you are exporting In/Out rather than the full sequence, coming in a few seconds shy of the full sequence length. Why not trim the sequence and export the entire sequence? Not sure if perhaps this has anything to do with the issue. Also, you said you exported AC3 but the export setting shows PCM. Have you tried exporting a PCM (.wav) file? Only takes a minute, try that and see how length comes into Encore. Encore will trancode the .wav to AC3 for you, so no harm trying this.
Thanks
Jeff Pulera
Safe Harbor Computers