I`m the in the same problem as you were. I installed NET 2.0 runtime just in case. No matter what i do Windows 98 SE see the card as PCI VGA, not as Agp VGA. I switched between chipset drivers, old vs new, nothing.
The only thing that is i havent done cause i dont thing it will make any difference is to maybe return BIOS version into older, but that makes no sense since this Gigabyte 9600 Pro that i using is from 2004 model.
And this is 3rd 9600 that i try to make work with my Pentium 3 (previous versions saw cards as AGP, one had bad caps that needs to be replaces, other (XT version) died after 10 days of usage.)
Man, its getting totally ridicilous finding working 9600. I may just give up and search for different card. All previous cards i tested never saw card as PCI VGA before. 🙁
I guess i`m again out of luck.