Perhaps the script is not being called in secure way.
Specify below path in post-customization script under pool setting and try again:
Make sure start.bat is placed under C:\script folder on master image. Also if you run the script manually on master image manually, how long it takes to run? By default, ClonePrep terminates a script if the execution takes longer than 20 seconds. You can increase this timeout limit. For details, see Increase the Timeout Limit for ClonePrep and QuickPrep Customization Scripts.
Alternatively, you can specify a script that runs another script or process that takes a long time to run.