Something bothers me about the set screw suggestion - if the focusing ring was out of position, it would display an incorrect distance, but the problem isn't the distance displayed vs the real distance, it's that when the image is focused on the ground glass in the pentaprism, it isn't focused on the film. Moving the focus ring will change the indicated distance, but won't affect the GG / film plane problem. Am I missing something?

What model is the camera?