Mobo may HD issues

Ok heres the problem. While using my machine to format extra drives I attempted to format one that was bad. My system quit working altogether after that with or without the extra drive connected. I have three drives in my system. A OS drive (80gig), a program drive (80 gig), and a file drive (120 gig). The OS drive is connected to the mobo and the other two are connected to separate channels on a ATA controller card. I attemped to reformat and reinstall windows on the OS drive and the format failed several times. So I disconnected all the drives and tired again to no avail. I then tried to do the same with the Programs drive with the same results. I took a 20 gig drive out of an old machine that I know is good and tried again with no luck. Thinking that something may have screwed up my bios I did a recovery flash and still the same. I have been double checking all the connections everytime. I am out of ideas and any help would be appreciated.