The following warning was added to ISE 8.2i Project Navigator to flag a condition that previously prevented a project from being opened.
"WARNING:ProjectMgmt - Problems were detected in the project file during open.
If you experience problems with data inconsistency we recommend that you run Project -> Cleanup Project Files."
However, the warning is incorrectly triggered by the use of VHDL Packages with declaration and body in the same file with the same name or by an Entity/Architecture pair in the same file with the same name. Selecting Project -> Cleanup Project Files does not eliminate the warning message.
This problem occurs because the test for duplicate Design Units (DUs) only matches based on the name of the DU. In these cases, it also needs to match based on the type of the DU.
This problem has been fixed in the latest 8.2i Service Pack available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jsp
The first service pack containing the fix is 8.2i Service Pack 2.