Hi Ram,
I've had this issue before. Use tcode GRFNMW_CONFIGURE to remove items from MSMP when you face this issue.
I also prefer to transport MSMP via this tcode as well. While in Change mode, go to Table View at top menu, and switch to "Transport". Choose/Create a transport and then you can manually save each settings table into the transport. If you try to transport MSMP the standard way, sometimes changes do not push through the landscape correctly.
-Ken