You should have another look at the rear brakes to make sure that you have everything installed correctly. If you do, then the pads may be made so that they do not fully contact the rotor. They will in time, but it may be faster to sand the pad to better match the rotor. I really most suspect that the pad is somehow cocked or that there is something between the caliper and the backing plate of the pad that keeps it from setting in place properly. If the pads have shims, are they properly installed?