Did you confirm you have it wired correctly? It sounds as if the AT is trying to make Cyl2 act as Cyl1. Make sure you have AT1 connected to the front cylinder and AT2 connected to the rear cylinder. The 1 and 2 on the Autotune modules are not marked very well, but they are there.

 

Sorry guys for the late reply. I checked everything again and again. The system is working right. I also checked the baffle of propipe bp. It's baffle completely closes the pipe and the gas going out from holes around it. I use supertrapp at my fatboy with open end cap. Can I solve my problem with a supertrapp exhaust? what is your opinion?