A major version number change is required because of changes in the default values of parameters in the MPD file.
The latest release (ppc440mc_ddr2_v2_00_a) will include all changes and update to ppc440mc_ddr2_v1_01_a.
The latest ppc440mc_ddr2_v2_00_a core was released in the EDK 10.1 Service Pack 2, available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jsp