This is something that I see and get asked about often, eyes light up when I tell them how to fix this.
What happens is that a user will produce Gerber and drill files centered in the bed in the scale & position dialogue and when they are imported into a Gerber viewer i.e. GC-Prevue the drill files are offset from the Gerbers.
This is not really a big problem as they can easily be aligned, but is would be nice if they simply lined up correctly - and they can so how?