I am unsure what is happening with the lengthening of your audio, but I can tell you that if your timeline has multiple AC3 clips in the audio track, Encore needs to transcode your audio into a single file for muxing. Your 5.1 audio then becomes a stereo file, as Encore does not support the AC3 license for 5.1 encoding. At least that’s my understanding as to why, but the facts are certainly true: If you want to stay in 5.1 when you author, you need to have a single AC3 5.1 file in each timeline- no edits. I hope this is helpful.