I do not know if you have done this yet, but you must set up the HD to be a slave. This is usually done through the PIN settings. If this is the problem you will have to look up your particular hard drive to get the neccesary help. Be warned though that the sites aren't always easy to understand.

Also the way it is hooked into the computer matters as well, which means you need to know how your particular motherboard works... although this is usually not a major issue.

As for it being a problem with linux itself... I have never had any problem once the HD is set right.

It is hard for me to explain it without being there to access it myself.