so is the data backed up? and is it possible to do a low level format (i.e. it's okay if you loose all information on the drive)? if so definitely do a low level format as it will also erase any partitioning scheme that was previously on there.
Also, are you saying you have reinstalled windows? if everything is still intact then i would do a repair install because i would think that would fix it with a minimal amount of data loss (normally none).