do as suggested by Xlphos check your jumper settings..were you able to boot from your dvd drive or not? if you were able to boot then i suppose it could be on your OS..your mobo comes with the disc...

i suggest you use dvd disc or either thumb drive.. no problem with external hdd but as said by Hughv must be careful..mishandling the hdd will loss all your data..

but if you're dealing with files...

check out this link...
http://en.wikipedia.org/wiki/Advanced_Host_Controller_Interface

AHCI..one of the controller for HDD interface...
or you can try searching the web AHCI vs. IDE