What causes brakes to pulse or shake when applied?

If they have been turned twice, then they are to thin & need to be replaced. The thinner they get the quicker they warp.

Uneven/over-torqueing of lug nuts will also cause warping. Replace with new ones as suggested and use a torque wrench to tighten the lug nuts. Clean new rotors with soap and water rinse good and wipe dry with lint-free cloth or compressed air - better than using brake-cleaner for new rotors and pads.