There could be several different reasons...
Usually the biggest culprit is the shoe itself...You need high quality shoes with stiff soles, usually fiberglass or carbonfiber soles work the best. My guess is your right leg is more powerful than your left one so you are exerting slightly more force on the right downstroke compared to your left one. Usually cleat misallignment will cause knee pains more often than hot foot but it doesn't hurt to check it. Also are you using a road or mountain system? Road cleats are usually more comfortable as they spread the force in a larger are compared to the mountain cleats...
So does that mean we're talking about SPDs, the little metal things that are recessed in the profile of the sole of the shoe?
You need an Allen wrench to change the position. Make sure they're tight when you're done or you may end up leaving your shoe on the bike.
Another solution may be to move to pedals with a combination platform and clip-in mechanism, like the Shimano 525s, at least for the trainer, to distribute the weight a bit better. I thought someone was selling some on here (don't remember if they sold . . .)
Dana said:I have a pair of Sidi's, but I think they're mountain shoes because they have the cleats on the bottom. I feel stupid asking this, but how do I change the cleat position?
Do you get hot-foot when walking, or just on the bike? Do your toes go numb after a while, or no?