Magnasight is not a grain focuser in a traditional sense. It projects the image on a ground glass. What looks like grain is grain of the ground glass, not the image. That said, there is NO adjustment.
I am not sure if you are really seeing focus difference.
While I do not use it anymore, I did have Magnasight at one point. Now I use Microsight by the same company.
Is it possible that your enlarger is out of alignment that depending on where exactly you place your focuser, it'll tell you different results?
Or, is it possible that your enlarger drifts? Mine does, so if I want long enough after I focus it, it'll be out of focus.
My near sight is affected quite a bit. But I am able to use grain focuser quite nicely by taking my glasses which adjusts my far vision off.
I think you'll first need to visit your optometrist, then figure out what to do. I'm afraid, otherwise, it'll be a guess work.