The file gene_association.fb conforms to the standard format specied by the gene ontology consortium and so should be indentical in format to the GOA file. See http://www.geneontology.org/GO.format.annotation.shtml
for details. If you are still having problems, please get back to FlyBase with more details for how the format differs from what you expect. Similarly, if there are any problems with the content of the file then let us know.