It could be Workbench was installed to a partition with lower boot-priority than another. You must go into the early startup-menu and check the boot priorities of your hard-drive. By judging your problem it sounds you are booting from an empty partition, try to type in dir[enter] and try to give us the output.
If the boot-priorities are wrong, you can manually override them in the early-startup-menu each time you reboot, to change them permanently you must use hdtoolbox.
To get into the early-startup-menu hold down both mouse buttons during reset.
