OK, so the first three bytes of C000.BIN are 55 AA 40. 55 AA is the signature bytes for an option ROM, 0x40 * 512 is telling the BIOS to expect 0x8000 bytes, putting the end of the ROM at 0xC7FFF. (And, in fact, the ROM is empty past 0xC78B3.)
Mysteriously, C800.BIN is entirely filled with FFs. There's nothing there. The VGA card appears to be playing nice here. (That doesn't mean that there isn't some other conflict, but...)
What model is the HDD controller, and can you install it, and run the commands again? C000.BIN should be identical, I'd expect C800.BIN to be different. No need to connect the HDD, just insert the controller.