Ron, the unit doesn't turn off when done autotuning, it just goes back to the regular program (not flashing At). Also, when it goes to step 2 (225), it's probably not done. It will continue until it finishes, regardless of the step.
You can autotune with any program. Try it with your normal brisket program, if you want. I'd probably just try a cook with the settings you got, and see how it does, before re-doing the tune.