Pedals: are you using clipins?
If yes - check the positioning of your cleats on the shoe. If they are scattiwompus then it's putting an "un-natural" angle on your pedal stroke.
When you run or walk whats the position of your footstrike?
Sample: Using myself - I toe in (from the hip)... when I first got clipins (SPDs of the LOOK or TIME variety), the cleats were installed "straight". It caused pain in several places for me; shins, knee... and my feet felt "wierd" in the pedals.
I had one of my infrequent brainstorms one night and fiddled a bit. I re-mounted my cleat so that the position allowed my feet to point the way they wanted to. End of problem... except I hated the pedals (but thats another story).
I switched to Speedplay (X2's) which are free floating and I don't worry about it anymore.
spazz