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I have been troubled with a rubbing rear brake on my 250 N/C , Its not consistant and goes away if i loosen the axle nuts. I notice that i have to squash the swinging arm in a fair way to tighten the axle, and am thinking the fork ends may not be parallel when its all tight putting a strain on the plate, does anyone have to use spacing washers against the hub or sprocket?.I have also been seeing wear on the face of the gearbox sprocket so someting is out. Should the rim sit equally between the rear susp units?

Sounds fishy to me, it should all line up nicely. Spacers should definitely not be necessary. Are you 100% sure that nothing is twisted (frame, swingarm) and that the swingarm bushes are reamed 100% square? Is it definitely the original swingarm?