I had the same problem and mine turned out to be my saddle. Once I found a saddle that fit my sit bones properly (I tried four different ones) my feet are much improved.

I was riding this past weekend with a guy from my bike club and he told me that rounding out your stroke also helps. I have been working on this skill as of late as well. I rode 25 miles on Sunday and my feet didn't bother me at all.