Are you using Windows Vista 'Complete PC Backup', Apple OS X 'Time Machine', or something else ? (Including Vista 'File Backup' and Windows OneCare Live Backup, etc).
Generally speaking (assuming Vista here) each PC it backs up will get put into a differnet subfolder (so long as they each have a different 'PC name').
Some 3rd party software likely works in a different way (ie: It may replace the backup store on the drive when used on a 'new' or 'different' PC).