Scripting

can you run cacls.exe directly in your package instead of using a batch file?

Also in case you're using SCCM, have you selected to allow the program to interact with the user?

Also pls check if the custom action is set to Deferred Execution in User context.

Assuming you are using the KBOX, you want to make sure that the deployment is completely "silent" during the installation on the target PC.  Typically, this issue is due to some part of the installation not being silent.  For the KBOX, you can always mimic the Local System user account by following this article -> https://www.kace.com/support/resources/kb/article/How-to-mimic-running-a-script-as-Local-System-User-Scripting

Could you repackage the batch file as an exe so it doesn't pop a command prompt? I've seen this help before with similar-sounding problems. http://www.itninja.com/link/batch-to-exe

I ran into a cmd box coming up when running cacls and was almost at the point of sending keys to the command when I found this: http://www.autoitscript.com/forum/topic/12318-automate-a-confirmation-in-dos-command/  Basically, you enter echo y|cacls to pipe that confirmation to cacls to make it run silently. 

I ran into a cmd box coming up when running cacls and was almost at the point of sending keys to the command when I found this: http://www.autoitscript.com/forum/topic/12318-automate-a-confirmation-in-dos-command/  Basically, you enter echo y|cacls to pipe that confirmation to cacls to make it run silently.