When I generate a multi-controller Spartan-6 FPGA MCB design in MIG 3.1, there is a problem with the GUI that only exists when controllers C1, C2, and C4 are selected. In this case, the C4 controller can only be selected as DDR2 SDRAM.
This is an issue with the GUI. There is no reason that C4 would have to be a DDR2 interface.
This issue is scheduled to be resolved in MIG v3.2.