I am targeting a Virtex-5 part and my software application in the "system.bit" file does not work, but when I download the ELF through XMD, the application does work.
There is a know issue where Data2MEM does not properly merge the ELF into the ".bit" file. To work around this issue, run BitGen to merge the ELF into the place and routed NCD file to produce the ".bit" file:
bitgen -bd <file>.elf <PAR>.ncd <system>.bit
This issue will be fixed in a future service pack.