Did you do the proper bedding procedure? I did so carefully, that I never let my brake pads touch a stopped rotor at any time for at least 2 weeks. I would slow to about 2mph then drift to a stop in neutral everywhere I went. It was a pain in the ass but I hate the pulsating brakes. It is essential to do the proper bedding procedure, however I'd say I went overboard for perfection.
I bedded mine for over an hour one night
I did what you did. Keep in mind this didn't start until months after and it's only occasionally, not always. I might try the bedding process again.