That is not the case with mine. The screws with a tapered head replace the like screws, and the round head screws the same, they should all be 4-40 screws I think. They should all be the same size.
Are you sure they are physically smaller, or are you over tightening them and stripping the threads? If yours are actually smaller you may have gotten the wrong screws for some reason, maybe Nitro TC3? I dunno.