well lets start with the harddisk itself...
the platters inside of a harddrive have markings on them divided into tracks and sectors,so if the markings get faded then that will yield a bad sector error.....and since the tracks and sectors of harddrives these days have different patterns on them, and no longer have the same sizes on each track, these markings are done at the factory, which is called low level formatting...now since all floppy disks are the same, when you format them, the format will write the actual tracks and sectors cause they are all the same having 80 tracks and 18 sectors (9 on each side), but now with bigger harddrives and the newer technology you can no longer keep a fixed amount of tracks and sectors cause if you did we would be still using a 512meg hard drives to the day
so the new (well not so much new anymore) technology called zone bit recording can now put a smaller number of tracks near the center of the disk and the number increases as you move to the outter edge of the disk....so with that said, this is why the factorys that make the harddisks do the low level formatting and put these track and sector markings on the disks at the time of making....
so now a days when you are formatting your harddisk all your doing is writing a boot record, the file system, and the root directory to the disk....and thats it...
....sooo if your disk has bad sectors there is one of two things i will suggest....either you could get a utility program to scan the disk for the bad sectors and get it to mark the sectors for they won't be used, or you could get in touch with the manufacturer of the harddisk for a program that could perform a low level format on the drive...
:::NOTE:::
a low-level format could be a catastrophe, and it could permenently destroy the drive unless the drive controller BIOS were smart enough to ignore the command...
so don't try and use a program that you think could work or a program that is from another company, etc, etc...make sure if this is done that you get it from your manufacturer...