I've seen this happen with BMW rotors. The problem seems to be build up of baked on brake pad dust from previous pads, cooked on the rotors. It reacts with the new brake pad compound and makes horrible noises. I've found the the following to help:
1) Follow the manufacturers recommended "bed-in" procedure very closely. It usually goes something like, accelerate to 10 mph, slow using minimal brake force. Accelerate to 15 mph, slow with minimal brake force and wait 20 seconds. Repeat in 5 mph increments until you're going 50 mph or whatever is reasonable in your neighboorhood/town/locale.
2) Replace your rotors when you move to a different pad compound. In the event that you don't want to make the investment in new rotors (especially when the old ones are just fine) you could try taking the rotors to a shop to have them "turned". This will decrease the life of the rotors slightly, but should clear off any of the old baked on brake pad nastiness.
Moving back to OEM pads might work, but it may continue to react with whatever the current pad leaves behind.
Good luck!
-=Nick
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