foot pain and cycling?

[bkdjr2000]

I started getting into cycling (both on and off road) a few years back. At one point I was going pretty hard on road, maybe doing 30 miles a trip x 3 per week in hill country (not Lance, but good for a beginner). I was also walking a bit on my off days and my left foot got to hurting pretty bad and was getting numb on the outside ball. I didn't think about the cycling causing it, but winter came and it bothered me all winter even though I wasn't cycling. Next spring I didn't get back into cycling and by summer my feet were pretty much OK. Fast forward 3 years and I got back into cycling (or at least serious enough to clip in). Immediately the numbness and pain returned and I realized what had caused my problems a few years back. My feet are pretty dry and cracking a bit so now I am treating that, but I wonder if there is some nerve I am pinching. It only really seems to be a problem clipped in, if using freeride pedals it doesn't bother me, or at least not as bad because I can put my arch more on the pedals instead of my ball. I spoke to my family doc about it and he wasn't much help. Anyone have any ideas or similar problems? I am hoping its dry skin being aggravated by the pressure as I love to cycle. Maybe better shoes or custom make a mount over the heels?