It's very common that Drill files exported from PCB CAD tools, do not align with with the Gerber files (I'll never know why). Anyways FAB 3000 has several tools to align the drill over the Gerber files. Here's a few links from the Help Center,
If possible please send me a sample set of Gerber &Drill files you have. I will create a tutorial movie showing exactly how to import the Gerber and Drill to have them properly loaded.
Thanks again, and I look forward to hearing from you.
The drill file requires that you use the setting "Trailing" for Zero Suppression. The drill file itself doesn't contain anywhere that Trailing is required (unlike Gerber which requires that information in the header). Since the zero suppression requirement was not defined in the drill file, FAB 3000 used the default which is "No Suppression". By setting the FAB 3000 default value to "Trailing" it will become the new default, and you should be fine for all similar jobs you import in the future. Here's a quick tutorial movie showing me perform this task: