If you didn't have both drives in the computer when you installed it, the boot configuration data won't have both, hence those programs can't see it.
First, raise a command prompt in admin mode and type bcdedit, to see if it finds both installation (probalby not).
If you can repair the instance of the OS that is not showing (back up your personal data if you have any there), it should add it to the BCD and you would be able to see both. You can also change names etc in the boot screen so you know which is which. This document from Microsoft has all details about BCDedit: http://download.microsoft.com/downlo...edit_reff.docx