Mike, now that you explained how you have yours setup, it makes sense now. If you read the instructions manual (if you have it) you will see that is says to 'disable' the PWM option for BAC if you are using it for idle speed control. That way it uses the settings in the 'input/output' page.
This all from reading the manual. I use mine for the ALS since the only elecrical draw on my car is my stereo
Jay