Running BitGen with the "-intstyle" option prevents the display of all warnings and error messages in the command window. Although ISE might not report the BitGen error/warning message in the console window, it is recommended that you check the ".BGN" file to ensure no DRC issue has been found in the design.
To work around this issue, run the BitGen command via command line without the "-intstyle" option, or check the BGN report to ensure a bit file has been generated.
This problem has been fixed in the latest 6.2i Service Pack available at:
The first service pack containing the fix is 6.2i Service Pack 2.