Reallocated sectors - wrong disk geometry?

Hello all,

I have a problem here that I've been unable to fix / completely understand using my normal methods of web searching, so I'm hoping someone here could shed some light! I'll start from the beginning...

I've been sorting out a machine that was given to me so that I can use it as my main desktop computer. I upgraded the RAM but the module was bad, caused screen corruption and didn't boot, so returned it. As part of me attempting to get it to work I upgraded the motherboard bios to the latest version. The computer is an Emachines 420 (also known as T2682) and has a Trigem Imperial GV motherboard with a Pheonix bios (now 4.0). The bios upgrade added a new menu item, "Large Disk Access Mode: [DOS] or [Other]. In order for the hard disk to boot (instead of a flashing cursor in top left), this value had to be set to "Other".

Here's the hard disk bit. After a couple of days I noticed the hard disk taking a long time to access some files when being used on the network, it was also making a different noise at those times, I can't remember quite what but just more intensive. This hard disk is a Western Digital Protege WD800EB, 80Gb 5200RPM. I thought something could be up, ran chkdsk and HDTune scan and found 4 bad sectors. HDTune also gave SMART warnings 5 (reallocated sector count), C4 (reallocated event count) and C5 (current pending sector) - the latter claiming disk was unstable.

This was clearly not good, so I connected the hard disk from my old machine (actually a newer disk from an upgrade) as a second hard disk (using cable select both drives) with the view to Ghost drive to drive. This disk is a Western Digital Caviar WD800JB, 80Gb 7200RPM. I ran Partition Magic 8.0 in Windows XP and received two separate error messages, each saying that each Disk appeared to have partitions created using a different drive geometry (255h 63s), a serious problem that can lead to data loss etc. As I had used partition magic only a few weeks before on the original disk to split it into C: and D: (primary and logical) without this error message, I presumed it had something to do with the bios upgrade. However, selecting DOS on the Large Disk Access Method would just result in the blinking cursor.

Well I deleted all partitions on the new drive (WD800JB), created one primary and formatted it. Partition Magic no longer brought up the geometry error for this disk. I used Norton Ghost to replicate the old disk (WD800EB) onto the new (so 2 partitions) using disk to disk method. However, I then ran chkdsk on the new disk and this also brought up 4 bad sectors which weren't there before and HDTune gave SMART warnings 05 and C4 (05 = current: 199, Worst: 199, Threshold: 140, Data: 5; C4 = same current and worst, data: 1). The Data values for the code 05 (data = 5) were identical for the old and new drives.

Thinking this was still an issue with the Bios setting, I removed the original hard disk (WD800EB) and replaced it with a Seagate ST340014A, 40gb. I copied across the active system partition from the other disk (WD800JB) and got it to boot - however I noticed that the Seagate would also boot with the Bios Large Disk Access Setting set to DOS. I therefore backed up the logical partition on the WD800JB deleted both partitions, created one primary and formatted it, thinking that the geometry might now be set right. This got rid of the bad sectors, however, on copying the data back I still have SMART warnings 05 and C4.

So I'm a bit stumped. I'm not sure if this is still an issue with the disk geometry not being set right, but I don't really know how to check this. Or is it just random coincidence on two very similar Western Digital hard disks? This issue really is at the top end of my level of understanding so any help would be appreciated!

Regards, Matt