When I run Data2MEM on the command line, an incorrect ID code is written in the BIT file for all Virtex-4 devices. (Direct BIT file replacement of the BRAM contents is not supported for all Virtex-4 devices.)
You can work around this issue as follows:
1. Add the BMM and ELF/MEM file to the ISE project.
2. Run Project -> Cleanup Project Files in ISE.
3. Run the Generate Programming File in ISE.
This will properly update the BIT file with the ELF/MEM contents.