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?
It's easy really, just make a change to the .usr files that you use.
Within the RS274-X.USR and Excellon2.USR files there are XHIGH and YHIGH values that by default are different - I assume that this is because the photoplotter machine had a different bed size to the NC drill machine.
Simply edit the files in Notepad to read the same I.e. 24000 in both files - this gives you a 2' square bed. Or if Metric - try 500 for both.
Then your drills will line up.