I was having this problem as well, and this post thread got me started in the right direction. After investigating further, I found a MSKB that describes the problem and has a workaround.
http://support.microsoft.com/kb/2796086
In a nutshell, you can change a registry setting and the CCMEVAL.exe nightly task will stop breaking the MP.
Uninstall the MP role, change HKLM\SOFTWARE\Microsoft\CCM\CcmEval\NotifyOnly to "TRUE", reboot, and reinstall the MP role. You don't have to uninstall the CCM client from the MP server.
This is supposed to be fixed in SCCM 2012 SP1, but I haven't installed it yet to test.
I was having this problem as well, and this post thread got me started in the right direction. After investigating further, I found a MSKB that describes the problem and has a workaround. http://support.microsoft.com/kb/2796086 In a nutshell, you can change a registry setting and the CCMEVAL.exe nightly task will stop breaking the MP. Uninstall the MP role, change HKLM\SOFTWARE\Microsoft\CCM\CcmEval\NotifyOnly to "TRUE", reboot, and reinstall the MP role. You don't have to uninstall the CCM client from the MP server. This is supposed to be fixed in SCCM 2012 SP1, but I haven't installed it yet to test.