The first important question is whether you're using SimpleTemplate or IterativeTemplate. If you're using SimpleTemplate, then your only problem is Motor Safety. If you are using IterativeRobot, you will need to restructure your code to remove the delays.
Here's a description of motor safety:
http://wpilib.screenstepslive.com/s/...safety-feature The example Java program disabled motor safety in autonomous and enables it in teleop. See
http://wpilib.screenstepslive.com/s/...ot-programming