I wasn't aware that ANY motherboards were ever produced which actually offered full x8 functionality on their AGP slots.. But never mind that
let's see...
Both of my MSI boards use the DELETE key to access the BIOS, but also, both my boards use an AMI BIOS, not Award. Does DELETE work for you?
The other menu you describe sounds like the BOOT menu, where you can select the boot device. I access that with F-11 on mine.
As to why the machine will boot with one AGP card and not the other, really sounds like a hardware incompatibility, though I can't suggest what exactly it might be. Like you, I would think that either card should work find, if they are both AGP and both fit correctly in the slot.
You say you did reset the CMOS once already, so I suggest that you try whatever you need to, to get back into the BIOS, and make sure the option for "BOOT VIDEO CARD" or whatever it''s called, is set to AGP and not PCI, or you will definitely continue to have this problem.
Best regards,
Sasha