As Leedsman often says, uneven deposits of friction pad material transferred at prolonged high temperatures are 99% of the cause of thickness variation and brake judder / flutter. The only other [infrequent] one I've come across is individuals who use home or garage based high pressure washers to clear dirt and particularly winter 'salt' from the disk / ABS sensor area leading to a 'warped' disk.

 

I had a similar problem on my 2004 Neon.Replaced pads and rotors, but the problem persisted. Turned out the problem was dirty ABS wheel sensors. I cleaned the sensors with a brush and paraffin and problem solved. The sensors are on the inside of the front wheels. To diagnose if the problem is ABS, remove ABS fuse (in engine compartment) Drive the car (remember no ABS!) and test the brakes. If the vibration is gone, problem is with ABS.

 

i agree, this time change the calipers as well as rotors and pads. get them from Prime Choice auto.ca or com depending if your in Canada ir US. free shipping and 1/4 price of anywhere else. http://www.primechoice.com/