[Chris Hibner]

One possibility is that the autonomous code is taking so much CPU time that it is slowing down the periodic tasks loop. There is a VI that is supplied by NI that will report the actual time that it takes to run each loop (I can't remember the name right now, but if you look in the vision processing example, it is included there). Place that VI in your periodic tasks vi and run your code using the play button. Run in teleop and auton and see if the loop time is different for each.

Also, I'm assuming you are passing your set point from your autonomous code to periodic tasks via a global variable. Is it possible that the global variable is being set in multiple locations? Run via the play button and place a probe on the set point signal just before the PID VI to check that the set point is staying constant.