[Alan Anderson]

The "Autonomous Independent" is run in a different way from all the other team-edited VIs. It is started by a special LabVIEW function when Autonomous mode begins, and it is stopped by a special LabVIEW function when Autonomous mode ends. If you just disable and re-enable without leaving Autonomous, the first run is not stopped, and if conditions are right a second copy can end up running at the same time. But that really shouldn't happen, and I don't think it's what is going on in your case. What is probably happening is that your encoders are not starting at zero when you run Autonomous a second time, and that's confusing your sequencing.

If you're going to cancel Autonomous without proceeding to Teleop, I think your best option for making things work properly is just to reset the roboRIO before running Autonomous again. You can do that remotely from the Driver Station.