I would also verify that the shoes fit and conform to the bottom of your feet well. When everything's right, your shoes shouldn't be any kind of a comfort limit.
I had the same problem - discussed it a bit in my blog (http://nathanbyrd.wordpress.com) a few months back. I finally resolved it with 2 things: (1) a proper bike fit, and (2) toe warmers on my socks, since the air coming into a fully permeable tri bike shoe this early in the season was contributing to numbness via freezing.