By default the system runs the CMD commands via 32 bit command prompt application.
However if you want to run them with 64 bit version you need to manually show the system the location of your .exe file using script execution directory.
Step by Step:
Please navigate to package editor during the package creation, than please choose the Script execution directory as presented in the picture:
That way you can choose the location by yourself.
The default location of CMD of 64 bit is: