Java CPU usage is different with cold startup vs. reset or deploy
 

I'm seeing some really weird behavior with the roboRIO's CPU usage.

When I first power on the roboRIO and wait for the robot to go into teleop disabled, the CPU usage hovers between 95-100%. This usage stays constant at 95% during robot operation, and the controls have lag. When I press the reset button the roborio, and wait for the robot to go into teleop disabled, the CPU usage drops to 40%. I do not see the high CPU usage after deploying code or pressing the reset button, only when I turn on the roborio with the main breaker and let the code run.

What could the difference between the two startup methods possibly be, and how can my code only affect one?