There are several causes:

1) hot-spots. Older or cheaper shoes and SPD cleats were often found to be a problem here. The shoe's sole collapes around the cleat causing a presure point under the ball of the foot.

This can often cause numbness or a burning feeling (often on the outside of the big toe).

2) Arch support. I am surprised even in my $150 shoes that the inside of the sole is nothing more than a thin flat pad on a nearly flat bottom. What can happen here, and is my problem, is the ball of the foot spreads out because there is no arch support. The partial collapsing of the arch and the excess pressure on the ball of the foot causes the nerves leading to the big toe to inflame and thus I get a sever burnning feeling on my big toe.

They make special pads that stick on the inside and placement of these pads is so they are just behind the ball of the foot to help prevent the arch from falling.

I found buying a sport-sole insert and cutting it, with some experimentation, has removed this problem from my right foot. My left foot still suffers from this but I'm still hoping to solve the problem with the cutting of sole inserts before I go to have special shoes made.

3) Straps too tight can cause the problem but be careful... Straps too loose and your toes will jab up into the toe of the shoe and cause other problems.

4) Also be aware that a toebox that is too big or too small can cause other problems... Bunions on the big toe and taylor bunions on the little toe. These can cause sever pain and can require surgery to fix.

5) Also your ankle support is important. With the flat sole cycling shoes your heel may be twisting. This happens on my mountain bike shoes to which a heel-cup insert helps. This can cause numbness on one side of the foot but more importantly this can lead to knee problems such as ITB syndrone.

I'm learning more and more about this as I push above and beyond 130 miles/day..