Usually that is because the computer has the Agent installed but does not have the DMPrimer installed. DMPrimer is required for the Deployment Manager to recognize that the Agent is already installed since it is the primer that responds to its query. This usually happens because the Agent was installed using a different method (not infrastructure deployment).
You can push the primer as a package if you need to. The primer install is actually an encapsulated MSI. You can extract it by running the setup executable and finding the install files in your temp directory during the first prompt, then cancel the install. You can then push it as a regular SD package and of course you can add the CA parameter to install it in a different location.
After the primer is installed you also need to copy the certificate file to:
C:\Program Files\CA\DSM\DMPrimer\
Or
C:\Program Files (x86)\CA\DSM\DMPrimer\
Depending of course on whether we are on a 32 or 64 bit system. This needs to happen after the primer is installed (so the directory gets created)
You can get the certificate file from the Domain Manager at :\Program Files (x86)\CA\DSM\DMPrimer
Steve McCormick, ITIL
CA Technologies
Principal Services Consultant