System.out.println is never advisable to use on the cRIO as the method gets called ridiculously fast and that's why the output gets jumbled.
I suggest you use the new smart dashboard for any output.
Check out WPILIBJ docs for more info:
http://www.wbrobotics.com/javadoc/ed...Dashboard.html
Basically import edu.wpi.first.wpilibj.smartdashboard.SmartDashboar d in whatever file you're outputting from and then instead of System.out.println, run SmartDashboard.putString("key", "value") and replace String with whatever datatype you're outputting.