This issue is caused by a design tool bug that incorrectly sets the MAP status in the project file (".ise" file).
In most cases, you can work around this problem by switching the project target device, then switching back to the original target device.
Optionally, creating a fresh project in a new directory and adding the same sources to the new project will also solve the problem. It is a good idea to frequently archive or take a snapshot of the project to be able to restore project status.
The user projects which have exhibited this problem all showed the same project/file disconnect.
This problem has been fixed in the latest 8.2i Service Pack available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jspThe first service pack containing the fix is 8.2i Service Pack 1.