What kind of pedals? I've been using regular spd pedals on a couple bikes ... everything was great. I added "campus pedals" to my Singlespeed run-around so I could use clips when I wanted or regular shoes. All of a sudden I just couldn't get my right foot in. Turned out that my mountain bike shoe's tread was interfering with the clip-in. I have an older pair of shoes w/ less intense tread that work just great. I think this would only be an issue with the campus pedal (which has a cage around the spd part).

So, if practice and moving the cleat around don't help. Maybe, just maybe, you need to trim a little more tread from near your cleat on the shoe.