See I just hooked up my new Hitachi ( yeah I said it ) to my MOBO and had to tweak the BIOS to get it to recognize both HDD's. I had to turn on a "combine option" [enables PATA and SATA] and then turn on my SATA to boot master SATA primary socket1. I have a recognize feature in this BIOS as well that recognizes new hardware.....which reminds me. What is your screen saying while doing a memory test and IDE seek etc...? What type of BIOS you working with? Did the External HDD come with software or is it just considered to be "plug-n-play"? Do all external HDD's show up under "My Computer"? (silly, but just curious)

Sometimes USB's are a little finicky..... I have four on this board and it only likes my top left one with some equipment.