That sounds like the motor safety mechanism is kicking in and stopping your motors because you are not setting the output powers quickly enough (the one second pause from your timer delay).
So, you have two choices. The simple solution is to disable the motor safety feature.
Code:
// Turn off drive safety feature as there are long delays between
// changing motor speeds during autonomous
drive.setSafetyEnabled(false);
// Your autonomous code
// Optionally turn drive safety feature back on (if you want it for teleop)
drive.setSafetyEnabled(true);
Alternatively, you can break your time delay up into smaller chunks.
Our team leaves the drive safety feature disabled for the entire match and rely on manual intervention to hit the Enter key when we need to disable a run away robot.