MIG v3.6 includes single controller support for DDR3 designs targeting CXT -1 parts. However, MIG does not include support for multi-controller DDR3 designs targeting the same parts. This support is added in the next release of MIG scheduled for ISE 13.1 software.
Solution
To work around this issue, you can generate multi-controller DDR3 designs targeting CXT -2 devices and then implement the generated design for a -1 device.