ECHO ON C:\PYTHON27\ArcGISx6410.1\python.exe \GIS\Automation_Files\PythonScripts\StopServices.py C:\PYTHON27\ArcGIS10.1\python.exe \GIS\Automation_Files\PythonScripts\ParcelJoin.py C:\PYTHON27\ArcGISx6410.1\python.exe \GIS\Automation_Files\PythonScripts\StopServices.py pause
This post is seven years old, hopefully you found a solution. If not, or for those with same problem, see this Esri KB article below. Basically you need to add Call in your batch file for each line. The KB article linked below has the details on why.
Problem: Batch files exit after the first Python command
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