Whew! Been running tests for the last couple of hours in an attempt to figure this out. Not done yet, but getting there.
First of all, after I put a blank chip into the card, OS X was showing a black rectangle in the middle of the screen shortly after trying to boot. Fixed that by booting with the shift key held down and running the FSCAPP program. Then the Mac would boot, but it didn't see the card in System Profiler at all, not even as a PCI device. So what I'm seeing with blank/corrupted firmware is a different problem than what you're seeing.
I ran UPDFLASH.EXE to flash the card with the contents of ROMFILE.1S2, but it work--still no PCI device. I then read back the chip and it looks like the DOS flasher didn't do a complete flash job -- it left off some of the end of the file. So then I put the whole file into a 256 KB file padded with 0xFF at the end (which is what it should be). Still no dice. At this point, OS X *still* didn't see the card as a PCI device!
Next, I used UPDFLASH.EXE to flash the card with my raw dumped contents of the original chip. This resulted in UPDFLASH claiming that it had an error flashing the chip. Caused a black rectangle on my screen during boot when I stuck the card in my G3. Shift key or not, same result. FSCAPP doesn't fix it.
Finally, I flashed the new chip manually with my programmer to contain the raw dumped contents of the original chip. Still black rectangle on screen during boot. Can't seem to get past that problem now...no idea what to try at this point. Something is causing OS X to crash, I think. Maybe it's a kernel panic, not sure.
Edit: Yeah, booted in single user mode and it is a kernel panic, the firmtek driver is causing it. Hmmm...