Originally Posted by ronny214
To expand on the answer given to you a bit, here is why. The JB4 intercepts key sensors and adjusts readings between the ECU and the sensors accordingly. Since it is all handled by the Juice Box (JB), that is what allows you to adjust on the fly. It just tells the Juice Box, "Hey, start compensating and adjusting for this type of performance now, please."
The Cobb AP on the other hand, and almost any flash tune for that matter, actually goes into the ECU and tells the ECU, "Hey, I need you to perform at these levels, so adjust and compensate accordingly." Since you are dealing directly with the ECU the car has to be in certain modes to accept new instructions.
Sorry, didn't want to make that too long of an answer but I really like to know the why of things so here's to hoping it helps others out.
EDIT: If anyone sees/feels that I didn't word something incorrectly, please feel free to expand on/correct it. I am by no means a pro tech/tuner.
Well thank you for taking the time to write this and expand on my question. You can never have enough knowledge on these forums. Appreciate it.