It appears that you are loading "old style" gerber files (RS-274D which was popular in the 90's) where the aperture used in the gerbers are actually contained in a separate file; and not embedded inside the Gerber file - like most modern gerber files RS-274X.
This means that you would need to determine which file is the aperture list and then go to menu: Setup | Aperture Table... and manually enter in each aperture. Afterwards your Gerber files with then have all correct line widths and pad sizes. Here's more information from the FAB 3000 user forum about RS-274D Gerber files: http://forums.numericalinnovations.com/search?searchid=16516081
If your aperture list is large (more than 20 apertures), FAB 3000 also has an "Aperture Rules Wizard" which can help automate the process of reading your aperture list files. You can check out the FAB 3000 Help Manual about using the "Aperture Rules Wizard", and here's more information on the FAB 3000 user forum: http://forums.numericalinnovations.com/search?searchid=16516134