As Kory said, please update your software, and then firmware for both your FlashScan and the customer's AutoCal to the latest pre-release software, dated October 5.
https://forum.efilive.com/showthread...ate-Oct-5-2014
E39A is a separate controller in the V8 Scan and Tune software. To ensure you do 'detect' the right controller, I recommend that after you update your software that you open V8 Scan and Tune software, then in the [F5: BBX] -> [F3: Tune] menu select open and open the Options_GM_Gas2.txt options file. Uncheck any controllers you do not require leaving you with E39A.
From there you have a number of options to send updated configuration files to your Customer for him to update on his AutoCal, the Quick Setup is probably the easiest method to use.
Cheers
Cindy