I have a new Seagate 250 GB PATA drive I got as a warranty replacement. It immediately started acting up. So when I saw you had MHDD for download, I burned a CD and tried it out. My original theory was that a fan I just moved (while installing the new drive) was hitting the drive and/or its cage. (I was hearing a lot of chirping noises and the entire computer would constantly pause.) Windows rarely boots until the drive has been spinning for some time.
This is bad because I have to shut the computer down while I sleep as it is in my bedroom.
I had MHDD do a scan just after I turned on the computer. I got over 50 on the item labelled ">500 msecs" and 172 IDNF (what ever that is). I then ran it a second time to see how much difference having it run for a while made. The scan completed much faster. All the times were lower and the IDNFs fell to 54. I also had MHDD do a screen shot, but I don't know how to read it. (See attached.)