A problem was found in Project Navigator where the wrong source in hierarchical design is selected as the design unit regardless of which source is selected as top. This problem has been seen most often when the "top" source files have been changed after some processes have been run or when using incremental design flow.
In most cases, running Project -> Cleanup Project Files will reset the project to the proper state and allow the correct top-level module to be sent to Project Navigator processes.
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.