Solution or Workaround
When Geocoding by Zip, the program utilizes the centroid.dat file in the Atlas GIS 4.0 root directory. This file is also utilized when Geocoding by Address using the Zipcode Match Method.
When doing a Query | Find | Location by Zip/Zip+4 the program utilizes the zip4.zhp file, found in the Geocode folder.
These files are also on the U.S. Address Finder CD that comes with Atlas GIS 4.0. If you have the Geocode Data Path set to your CD drive, you can keep the U.S. Address Finder CD in your CD drive when Geocoding by either Zip or Address.