Opening MMC certs and looking at the cert shows the cert is missing it's private key and in my case also the friendly name didn't carry over.
http://www.petri.co.il/forums/showthread.php?t=52766
Open the the certificate from the CA and on the details tab find the thumbprint field and copy it to your clipboard.
Now run the following command from a command prompt:
certutil -repairstore My "
In addition, in the MMC you can right click your cert and go to properties to assign the friendly name.