Nobody can tell you anything without proper system info and other technical details like audio files used, comp settings etc..
Hello SenseiBill - I had a very similar problem and received this reply from Tim Kurkoski on the Adobe staff:
There is a bug in After Effects CC 2015.3 (13.8) where exporting your composition via Adobe Media Encoder may not render the audio correctly. Audio can repeat itself at the end. This is only a problem with audio, video is unaffected.
The After Effects team is aware of this problem and are working on a fix. Until that is available, we recommend you either:
- Export compositions with audio using the render queue in After Effects to an intermediate file (ex., QuickTime with GoPro CineForm, Apple ProRes, or Avid DNxHD/HR codecs) and then transcode that file to the final format using AME. (Watch folders in AME are handy for this.)
- Export compositions with audio using AME CC 2015.2 (9.2). The project files saved by After Effects CC 2015.3 are compatible with previous CC 2015 releases (some new features will, of course, not be available). You can either add the composition in the AME interface, or open After Effects CC 2015.2 (13.7) and use the Add to AME Queue command there.
Our apologies about this bug.
(Under the hood: the problem is related to the new audio playback architecture, which is not taking into account the chunk size that AME requests for audio encoding. Should the composition length match a multiple of the requested chunk size, there will be no problem, but in most cases the composition length will not match a multiple of what AME is expecting, and AME fills the rest with stale audio that is still in the buffer.)
A temp fix I found is to make your comp a few seconds longer and set your work area to the length you need...
thanks to Szalam