I am designing a web site in which users solve puzzles as quickly as they can. JavaScript is used to time each puzzle, and the number of milliseconds is sent to the server via A
You asked a bunch of questions in your original question, I'm only going to answer one of them:
Am I going to have to use something that gets compiled, like Flash? (Yikes.)
Yes. Given your criteria: 1) 100% accurate, and 2) No possibility of user interference, you have to use a compiled binary.
Doesn't have to be flash though - I'd suggest a java applet if the thought of Flash makes you say "Yikes".