Your Gerber files may contain the circles, however Gerber does not have the NC data (i.e Tool Number, Size, etc.) that is required to export a proper Drill file.
FAB 3000 can automatically generate this information for you using the command "Gerber to Drill".
1. Convert Gerber to drill. ( menu: Fabrication | Generate NC Drill/Rout | Convert Layer to Drill...)
2. For the option "Gerber Layer", select the layer that contains the circles, review the other options and press OK.
3. A new drill layer has now been created. You'll now see "clear target" symbols where your Gerber circles existed. These are drill hits that contain a tool number, size, and everything else required to export a drill file.
4. Now export that new drill layer to a drill file (menu: File | Export | Drill).
Here's a related topic which may be helpful, https://numericalinnovations.freshdesk.com/support/discussions/topics/14000002300