This problem has been fixed in the latest 9.1i Service Pack available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jspThe first service pack containing the fix is 9.1i Service Pack 3.
It is important to note that even with this fix, the "Find in Files" process does not search the content of ALL files in the selected directory. It is limited to searching files used by Project Navigator and by tools that directly plug in to Project Navigator. For a more reliable search, include the specific file extension specified when using "Find in Files".