When I attempt to open an old project with Timing Analyzer in 10.1i, a dialog appears asking me to use Project Navigator to update the project. After this dialog, the Timing Analyzer dialog appears. If I try to continue loading the project, the same "Use Project Navigator to Update" dialog appears.
This problem has been fixed in the latest 10.1 Service Pack 2 available at:
http://www.xilinx.com/support/download/index.htm