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I use LuaSocket to get more precision.
require "socket"
print("Milliseconds: " .. socket.gettime()*1000)
This adds a dependency of course, but works fine for personal use (in benchmarking scripts for example).
You can use C function gettimeofday : http://www.opengroup.org/onlinepubs/000095399/functions/gettimeofday.html
Here C library 'ul_time', function sec_usec resides in 'time' global table and returns seconds, useconds. Copy DLL to Lua folder, open it with require 'ul_time'.