Ah, yes, I didn’t realize that your MOV files had the video track last.This should fix that. I’ll update all of the scripts.

@ECHO OFF
TITLE “Output 5.1 and Stereo AAC”
if [%1]==[] goto :eof
set Destination=%~d1%~p1
cd /d %Destination%
md AAC
cd /d “%~dp0”
:loop
ffmpeg -i “%~1” -filter_complex “[0:0][0:1][0:2][0:3][0:4][0:5] amerge=inputs=6[51mix]” -c:a aac -filter_complex “[0:6][0:7] amerge=inputs=2[20mix]” -c:a aac -map [51mix] “%Destination%\AAC%~n1”_5.1mix.aac -map [20mix] “%Destination%\AAC%~n1”_2.0mix.aac
shift
if not [%1]==[] goto loop