The default is No Compression (no codec). That could cause playback problems alone, but transcoding it should eliminate any playback errors. Before you do anything else, try putting it into a timeline, then right-click the asset in the project window and choose Transcode Now. Does that fix it?
If not, try a few variations: set audio to 48 kHz and re-export with No Compression. Does that play back better in Encore? If not, does transcoding it in a timeline as above solve the problem?
If not, then try exporting from AE using Microsoft DV codec. Does that play back better in Encore?