I have the exact same issue. AMD and Mobo transferred from old case to Antec, also switched from raid ide to a seagate ide. It doesn't recognize the harddrive on a cold boot. I turn off the power on the power supply switch for 5 seconds and then back on, hit the switch on the front and it is fine.
I'm going to check my bios but I think it might be the power supply, are you using the power supply that came stock with it?