I have a PacBrake on the exhaust, not a Jake, but I leave the switch on all the time. To engage, I simply touch the brake pedal. To disengage, I touch the accelerator. I also leave the Cruise Control switch on all the time. To engage, I press "set", or if it has been engaged already, "Resume". It disengages whenever I touch the brake, just like in my car.
I had some trouble with the Allison touchpad last year. While it was malfunctioning, one of the things it did was to behave more like you are describing. Once I had it replaced, I was back to the above described condition. Maybe you need to go to a service centre and have them read the codes in your Allison control pad to see if it is functioning properly.