When you downloaded the .obo file, was a .txt extension added? You need to remove that if so - the file will only work properly with BiNGO with a .obo extension. You may have to use the command line to do this on Mac - it seems to be particularly fussy about adding a .txt extension to ontology files.
Also, did you unzip the goa_human.gaf.gz file?
If you did all those and it still doesn't work, can you send a copy of the versions that do? The ontology should work fine as long as it has a .obo extension, though I am having issues with the goa_human annotation - other annotations work fine, so I'm wondering if something has changed since the old version that breaks BiNGO...
Tim