Thanks, Golden - the utility you linked to is only for FAT drives, and this is NTFS so it wouldn't work.
The Windows Bad Sector count is held in the MFT - not on the disk itself - which is why the /B switch works in Vista and Windows 7.
The way it works is - I gather, perhaps wrongly.....
1) Windows has a problem reading a sector (usually an ECC error) so it tells the Disk firmware that there's a problem. The firmware then retries the read.
2) After so many attempts, Windows gives up, and tags the sector in the MFT as bad, and then instructs the firmware to do the same on the HD.
3) Along comes the manufacturer's utility, and that can't see any problem with the sector on the physical read, so it unmarks it as a bad sector.
4) Windows still has the sector marked as bad in the MFT so ignores it totally, and still shows it in a CHKDSK report.
Note that this only applies to software failure (possibly caused by power spike/drop during read), NOT a hardware fail, such as a dust particle on the disk blocking reads (you can sometimes tell this, if a number of contiguous sectors are failing, and refuse repair by the utility)
The /B switch in Vista/Windows 7 clears the MFT table so that the implied /R can retest the sector readability, and /F can retest the data.
In theory, a simple reformat will clear a software bad sector, providing the firmware sectors have been reset first.
However - I made the mistake on this machine of not running the CHKDSK until after
reinstalling, updating and installing the required programs. I do NOT want to have to do that again in a hurry!
...and if I clone the drive, it will clone the problem.