For the aftermarket exhaust brake.
"BD Diesel has tested this kit with H&S, Bully Dog and Smarty box tuners.
EFI Live and other custom tuning must not disable the VGT operation. See information below.
The following is an example from a 2009 truck, others will be similar.
F1030 VGT Module Fitted must be set to YES,
E8756 Turbo Speed Sensor Fitted must be set to YES. All relevant P-trouble codes must be disabled."
Here are step to troubleshoot your BD brake.
1. Unplug the compressor and apply 12v to make sure it's working.
2. If #1 works, plug it back in and test the relay if its working or replace it with a known good one just for elimination process and also check the function of the regulator.
3. Open the control box then (make sure everything is connected and dash switch is on) and press the test button.
EB should be enabled. If not, you have a bad control box. I still think your tune is the culprit though for eb issue but BD sells the manual switch
Good luck! Btw, BD's costumer service is awesome, they took care of me when i had issue few months back.