The new HDL source is being incorrectly associated to "Simulation Only".
This can be fixed with the following procedure:
1. Remove the new HDL source from the project by selecting it in the Behavioral Simulation view and pressing the Delete key.
2. Select Project -> Add Source... and select the HDL source file and then click Open.
3. In the Adding Source Files... window, change the file association from "Simulation Only" to "Synthesis/Imp + Simulation".
If any ports are added to the new HDL source during creating in the New Source Wizard, the ".vhd" file will be correctly added to the Synthesis/Implementation view in the Sources window.
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.