This is really weird. I think I had a similar type of problem when I upgraded a PC with a larger HDD than the BIOS would support. In my case the FDD stopped working as well (Award BIOS), which doesn't really make sense as it is using a different conection to the IDE connection. Maybe they use the same chip on the motherboard?
Anyway, I managed to resolve the problem by installing the type of software that VictorKaum mentioned - which also has the advantage that you can use all of your nice new HDD. As far as I know all DDO software works in the same way, so it does not matter who manafactured your HDD. Completely baffled as to why this worked