I'm wondering if the height of the shoe tread is bothering you clipping in and out. Is the height of the tread higher than the cleat? I know that you mentioned that you can clip in although difficult, but wondered if you truly are not fully engaged when you are clipped in? Ive forgotton, do you have the same cleat on both shoes?

Mine seem to bother some as well,and think that I will trim down the shoe a bit. My shoes are a bit older, although never been worn until now.(Diadoras) But the height of the thread is definitely higher than the cleat which is obviously brand new.

At any rate, definitely keep us posted!