When you build a design in Base System Builder targeting a board with 2 DDR2 memories (requiring 2 MPMC cores), BSB will not connect the mpmc_clk0_div2 to the second MPMC.
This problem has been fixed in the latest 10.1 Service Pack, available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jsp
The first service pack containing the fix is 10.1 Service Pack 2.