Problem is some .NET components is required.
Open momcertimport.exe with notepad and go to the end of the file you will see this..
assemblyIdentify ........ "Microsoft.VC90.CRT" version="9.0.30729.1"
so you need to get this library install on the server (Microsoft Virtual C++ 2008 SP1)
Microsoft Virtual C++ 2008 SP1 -> 9.0.30729.1
Microsoft Virtual C++ 2008 -> 9.0.21022.8
Actually MOMCertImport.exe is just add an entry of certificate to the registry so it can be done manually..
1. Check the serial number of the certificates from Details tab (mmc -> certificates -> computer account)
2. Create new Binary Value "ChannelCertificateSerialNumber" -> HKLM\Software\Microsoft Operations Manager\3.0\Machine Settings but in the "REVERSE" order
Example : serial number is ab 12 cd 34 ef 56 -> enter it as 56 ef 34 cd 12 ab
Then restart health service
R1 -> "OpsMgr Health Service"
R2 -> "System Center Management"