I don’t know which format you are using so I’ll refere to it as FAT File allocation table. The FAT starts on sector one and expands adding a sector as space is needed. The FAT keeps track of where the firist sector of the file is located. The end of a sector has the address of the next sector the file is on, and the file is read like that until an End of File charactor is found. $FF
So a bad FAT would not show all the files being there.
A change in how the Bios interprets the stucture of the hard drive, can leave a readable FAT. Some of the files will be corrupted then or completely unusable.
Find a working computer. Take the hard drive in question and after opening the case, install the broken Hard Drive as a slave drive or a master drive on IDE 2.
Boot system.
Format broken Hard Drive.
Then, run scan disk on the broken Hard Drive.
If bad sectors are shown, either block them out, throw the Hard Drive away, or if it will store information and it is retrievable, use the drive as additional storage if the information is not critical.
Do not use the USB link for testing nor an external HD hook-up.
Harmonious Discord and GusNSpot give advice that is in general valid and good, but it’s clear they haven’t been paying attention to the thread at hand.
Nothing regarding what the OP said indicates that the problem is bad sectors! Nor is it the way the IDE controller chooses to format the disk. (harmoneous discord, welcome to the second half of the present decade…) The problem is the BIOS is not even detecting the hard drive, but windows is able to somehow reinitialize it and get it to work. This is probably due to a slightly broken HDD controller. (and no, it doesn’t have to be cracked. components can fail by themselves.)
There are two solutions. Randomly mess with bios settings to maybe get it to work. Or RMA the mofo.