The UART1 is used as default console by the Redboot and Linux. The Redboot will stop the auto-script if it received CTRL-C character before the script is run. Maybe the external device you connected to responded to the Redboot output and in turn stopped the Redboot executing the script. The Redboot can be modified to not output anything to the UART1 and not respond to inputs from UART1. You can also modify the Linux source code to not send anything the UART1. The Redboot source code is available at
http://arm.cirrus.com.