This problem has been isolated to a problem with the iMPACT plugin and how it registers messages. The ISE message manager is left in an incorrect state after this interaction and subsequent warning messages are not displayed correctly as a result.
The following are suggested ways to work around this issue:
- Use iMPACT stand alone rather than through the Project Navigator GUI.
- Close Project Navigator and reopen after every use of iMPACT.
This issue is fixed in the 9.2i Service Pack, available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jspThe first service pack containing the fix is 9.2i Service Pack 2.