The script associated with ModelSim processes is incorrectly overwriting the system_stub file. This causes a disconnect with the Project Navigator sources reference and the file is removed from the sources view.
This issue is fixed in the latest 8.1i Service Pack, available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jspThe first service pack containing the fix is 8.1i Service Pack 1.