I did not realise you where using the 3DR PDB so if that is the case, you will have a 4 wire cable that comes from the PDB to your Pixhawk, and another 2 wire cable. The 4 wire cable is for the signal line to the ESC’s, and the 2 wire contains power and ground. Did you connect them both to your pixhawk?
Otherwise it could be something to do with the timing setting the ESC’s directly that have been changed for some reason. My suggestion would be to set the motor timing back to high.
Also you should try changing the frequency to 16Khz
You can either use the USB-link board to setup the ESC on your comptuer, but otherwise read this guide here on how to program them using the audio tones menu.