I've had the same problem with my second pair of GTS11's. I'm now on my 6th pair of Adrenaline's without any previous problems. My first pair of 11's were great but the second pair I've had a pain on my right side, ball of my foot. I thought it was just me but then I tend to run on the outside of my feet. I'm finding that my feet ache more than my legs when on long runs...on the positive it give me something else to think about I guess!!
I love Brooks so am hoping that the GTS 12's are better.