The MIG design uses a BUFPLL_MCB component in the clocking structure for the MCB. This BUFPLL_MCB component had additional ports added in the ISE 12.2 software. Because of this model change, the MIG rtl generated prior to MIG v3.5 (ISE 12.2 release) does not connect these additional ports which causes these errors to occur during Synthesis.
The MIG v3.5 design must be ran with the ISE 12.2 tools. For additional information on the BUFPLL_MCB changes, see
(Xilinx Answer 35976).