There are a number of possible reasons why this message may be displayed.
The most probably cause is that the email address has already been registered in the system (perhaps associated with an organization other than your own) and the email address is therefore not available to be registered again. This can happen, for example, where a contractor is added for leave tracking purposes to their assigned organization but not removed again when the assignment is complete. A unique email address can only belong to one installation of Appogee HR at a time.
If you search the Employee list under Organization for the user's email address and you cannot find the user they will either need to be registered using a different email address or unregistered from any conflicting organization. If necessary you can send the email address of the user to Appogee HR support and we should be able to assist in tracking down the conflict.