I have had this problem for the last two years. Unfortunately I changed a few things at the same time and the problem went away, meaning I can't tell you what it was exactly.
I did switch saddles to a Ritchey WCS Streem carbon (which is like heaven), also got some Bontrager road SL's and moved my cleats all the way to the bottom position instead of all the way at the top of the shoe.
I'm going to venture to say it was probably the shoes and a little bit of the cleat position. It was always my left foot that would go numb after about 15 miles but now I can roll for hours without numbness as long as my shoes aren't tight. I also went up in size to a 10 when my last shoes were a 9.5. These Bontragers do have a massive toe box which I love even though my feet aren't very wide.