Mp3 is Not the ideal Audio file format to be used in after effects ,
Use adobe media encoder and convert your Audio to Wav
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Having a similar issue since upgrading to 13.8. I have about 46 AE projects created previously to 13.8, and every time I render out a comp via AME the last second of audio gets repeated. Example: If the audio at the end is a VO saying, "This is the end," what you here in the rendered out video is, "This is the end is the end." Previewing in AE does not do this. I'm using wav files. I've tried replacing the audio file, but it still happens. This only happens when rendering via AME, so this could be more of a AME issue. The only way I have been able to remedy this is render out a master via the render queue, then encode that master for web with AME. An extra step I would rather avoid.
AE CC 2015.3 13.8
AME CC 2015.3 10.3.0.185
I have the same problem but your solution works for me....thanks for the suggestion!!!