While fit can be an issue, your pedalling technique can also come into play. If you consciously pull up and wiggle your toes, does it make a difference? You could be doing a lot of pushing and not enough pulling.

Also, road shoes are usually stiffer than the average mtbike shoe. You could have a pressure point screaming because the sole is collapsing over the pedal. You don't say what type of pedal you're using, but some pedals have less "collapse" factor simply because they provide a larger platform -- like Look and Time.

Are your Shimano shoes built for biking and hiking or are they more like what a racer would wear? Very stiff sole and minimal lugs. The latter not only look more like a road racer shoe with lugs on the sole, but would be a whole lot stiffer than a shoe that looks more like a light hiking shoe.

I know, I know. All these factors to consider!