This problem occurs usually when a source is removed from a project and then added again.
Follow these steps to resolve this issue:
1. Right click on the file, select Properties, and change the association of the file from Synthesis/Imp+Simulation to Simulation.
2. Change the association back to Synthesis/Imp+Simulation.
3. Set as top level.
This problem has been fixed in the latest 8.2i Service Pack available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jspThe first service pack containing the fix is 8.2i Service Pack 2.