Thanks again for sending the sample files.
The reason for the missing pads is: Aperture List file is missing.
Those Gerber files are a very old format (274D), which does not embed the Pad shape information to use (i.e Apertures list).
Note: Typically for older Gerber 274D files, an Aperture List file is also included with the Gerber files. During Import, FAB 3000 will scan all available files to detect if any aperture list file is present. https://support.numericalinnovations.com/support/discussions/topics/14000019117
However in your sample files, there wasn't any Aperture File present.
Solution: Please look to see if you can file an aperture list file somewhere (it's usually included in the Readme.txt or separate file). Without the Aperture List it is impossible to guess exactly what shapes and sizes to use for the pads.