The BIOS may not have ID's the HDD when you have the HDD power cable disconnected. That won't hurt the HDD, it just isn't recognized during Phase 1 (System Confituration) of the startUp process.
What is the model # or your motherboard and how do you have your System HDD connected?
Your new video card must be working or you couldn't get to the splash screen and then clicked <del> to enter the BIOS setup.
Do you get a single beep code after the BIOS initializes all the hardware and before it trys to find the MBR on the system HDD?
Disconnect and reconnect both the HDD power cable and data cable for completeness. If that doesn't clear it up, I'd reset the BIOS to it's default settings and let the BIOS detect all the hdw a fresh.
You might write down any BIOS config settings you specifically set, so as to reenable them after resetting the BIOS.