Yes you have, but the firmware in the ESC is for Modified motors.
If you are going to run STOCK motors, and want to use boost timing, upload V3.0_110930_STOCK to your ESC
AHA! That explains why mine wouldn't go above 16° of timing. The stock version goes much higher.
I do have one thing that's still not clear to me. The software has 3 different "profiles" that can have different settings in them. Are these profiles stored in the ESC or in the program box?