The Spartan-6 FPGA MCB MIG design includes a script file, ise_flow.bat, in the output 'par' directory to run the design through implementation using the command line.
This script file is missing the -w switch in the MAP command which causes an error if the design has already run:
The -w switch overwrites existing files from previous runs.
Because this switch is missing, MAP will not execute.
To fix this issue, Update the ise_flow.bat parameters for MIG v3.2.
This issue will be resolved in the next release of MIG in ISE 11.4.