You can also check the drive using any type of Hardrive Managing software.
I use that partition magic (powerquest) and it is helpful when partitioning, formatting, and troubleshooting my hard drives.....
Its simple....... just start PM magic 8 and it reads your drives... gives you a picture on how your hard drive looks like.... partition size or filesystem, you can take care of the rest.... other than that.
Try using your WD Hard Drive Installation Diskette to format the whole thing, to your likings... and that shoudln't give you any problems. Transfer all your data to your huge 100gb drive and format the 40gb unless its where you have XP! installed.
I have two WD hardrives myself.... and use it when something goes wrong.... (something always goes wrong with xp)