I do not have ISE installed in my PC anymore , I am not so sure what can cause this issue. BTW :
1. Did you edited the UCF inside the ISE ? If yes, Could you please try to cleanup project files ? (PROJECT > Clean up project files ) ( Also try to delete and re-insering the UCF file ) Re do the synthesis and see if you still see the same error message. 2. If that is not help, I believe ISE is actually optimizing away your modules. If this is the case, please find if you your design keep asserting reset or does not supply a clock etc.