Has anyone experienced this propblem:
I use a digital multitrack recorder on location to record separate tracks for projects with complicated audio. I import and mix this audio in Audition. Once the mastered stereo audio is imported into Premiere and synced with the video, I use the rate stretch tool on the audio track to compensate for audio drift between the guide audio recorded with the video and the stereo mixdown from the multitrack. This keeps the audio recorded from the multitrack in sync with the video over long periods of time. Everything plays fine in Premiere. I then use dynamic link to send the finished sequence to Encore for DVD authoring. Once in Encore, the audio exhibits low level pops or clicks that are more noticable in certain places than others. I think some types of music mask the problem whereas soft ballads reveal the problem better. This problem flows all the way through to both Blu-ray and DVD masters. At first, I was not sure what caused the issue. I tried different audio formats and nothing mattered until I removed the timing change made with the rate stretch tool, so it is definately the cause. Keep in mind this is a very small rate change. Premiere shows it as only a .01% change and I'm not so sure that the dialog box just doesn't display enough precision. I think this is an audio processing problem with Encore and ultimately Media Encoder. I reported this to Adobe on the support page, but I don't get the feeling they care about my problems. None of the others have been responded to or fixed.
I have the same problem with separately recorded audio, and use (mostly) the same solution. (I manually type in the speed change, which I have discovered to be 100.04%) I have not had any issues with this method using CS4.
I do not use DL/AME for video encoding. The Main Concept engine Adobe has licensed just isn't the best encoder out there. So I export my audio separately to a .wav, then an Intermediate video file, and send that through a stand alone MPEG encoder. (Although I do let Encore handle the DD encoding for the audio.)