I am posting this to help others who may encounter this issue. I rebuilt our SRM environment on 4.1.2 and I was not able to assign a per CPU license to our protected site. The issue was that SRM in evaluation mode now defaults to per VM licensing so the protection groups I had created were using trial per VM licenses. I contacted licensing support but they said I should reduce the number of protected VM's to below what the conversion rate would be for per CPU to per VM licenses. That did not work. I ended up removing all of the protection groups, waiting for the licensing page to show no licenses used, and then it let me assign the per CPU licenses to our protected site. I then recreated a couple of the protection groups and the licensing page showed the correct number of per CPU licenses used. I read somewhere in the community after I had resolved my issue that they were able to contact support and get a test per VM license that allowed them to license the SRM server and then change it over to per CPU. I hope this information helps someone else avoid wasting the two days I spent resolving this issue.
By the way: converting SRM per CPU licenses to per VM licenses at a ratio of 1 to 5 is a load of crap. We are currently running over 25 VM's per CPU in our environment and there is no way I am converting my licenses over to per VM. I will happily stick with running vCenter, ESXi, VMUM, SRM, and everything else at version 4 before I spend a lot of money just to upgrade to 5.
