The libraries that Cartographica uses from ESRI that support interactions with File Geodatabase explicitly only support File Geodatabases from version 10.0 and greater of ESRI products. This means that the previous versions, support for version 9.3 will not work with Cartographica.
From investigation, the only way to make use of these databases is to either export the data to another format (such as shapefiles) or to convert the File Geodatabases using ArcGIS software on a Windows computer.
To do this using ArcGIS, you'll need to: