[Alan Anderson]

Moving the things out of the False case and into a final frame of your sequence should work. That'll make it stop interfering with the auto code.

But I have a different suggestion. Since your Periodic Tasks code works properly, why not just make use of it in Autonomous as well? I'd add a boolean global variable and OR it with the joystick button into the Case block. To fire the sequence in Autonomous mode, just set the variable True for a half second, then set it back False, to simulate someone pressing the button. That way you don't have the same function duplicated in multiple places, and if you ever want to change how the firing sequence works there is exactly one place to do it.