These messages are valid but can be misleading. In ISE Design Suite 14.1, the messages have been altered somewhat to attempt to explain which location or search path the license is not found in.
You can safely ignore the messages as the tool's function is not affected. If a license causes a tool not to run, an error message will be issued.
For an explanation on "WARNING:Security:42," see
(Xilinx Answer 33074).
For licensing search order, see
(Xilinx Answer 42507).