It seems to have stopped since I updated my ipad mini to IOS 7. It was driving me batty before and I didn't notice it had gone away till I just read this thread.
Did the update this morning on wife's iPad2 and, even using Safari instrad of my preferred Chrome, the performance improved; the Game Stop popup is now a little less obtrusive.
That said, I write this on my 2005-era PC using Explorer and Windows XL. No pop-ups whatsoever!