Did you adjust the headband already? You need to flatten it out, then shape it back. There should be very, very little clamp or pinching from the pads. Just enough to where they don't fall off, mine are loose enough that I think I could shake them off my head if I really tried, but not quite loose enough to fall off if I bend over. I had upper ear discomfort until I did this, and then it subsided considerably. THe first day or two after that I'd still get a little irritation after a few hours, but now it's perfect and my most comfortable cans to wear. Only thing as good are the Koss stuff.
The Geekria flats work pretty well for me if adjusting the headband doesn't work. I have them with the large opening facing out towards my ear exposing the driver, and cut slits in them like the stock flats. Sounded extremely similar, and I'm using those now to keep the stock pads in good shape even though I like the stocks better.