This is a known issue with AE 2015 and AME 2015. Adobe is aware and working on this.
Work-arounds:
1. Render with AE 2015 render Queue uncompressed and then use AME 2015 to compress the uncompressed render.
2. Use AE 2014 and AME 2014 for a direct AE to AME workflow. This problem does not happen with 2014.