Unless the magazines are staple bound, this is going to continue to be a problem, Perfect bound magazines have spines that are too thick to scan in tact properly without coming across this problem. That's why just about every perfect bound issue is destroyed in order to scan it. Staple bound issues are easier to scan in tact since you can fold the magazine over on itself in order to have both sides be the same thickness which reduces the gutter shadow and gutter glare.