The error you got was die to either a corrupted or missing command.com file. Basically, in english., it means that there may be something wrong with the hard drive. Before you go to bed, put in the WD diagnostics disc (you shoudl have one. If not, go to
www.westerndigital.com and get the Data Lifeguard tools). Do the extended diagnostics FIRST (second option). It will take from 10 mins to half an hour. If that passes, go to General diagnostics, and choose the long (extended?) option. It will take a VERY long time to finish this, so let it run thorugh overnight, whilst you catch some Zs.
Because your computer works fine with another drive, it has to be the hard drive. I'm not sure how, but it is. The thing above that I want you to do will scan it for errors.