Well, my purchase of a 53 reg 2nd Gen rx300 had one working and one duff key. The duff one did the locks only, and would not cancel the alarm if the car was locked by the other remote. To get the 2nd key working:
1. Tried new battery - same result. Light was already blinking when buttons pressed with old battery.
2. Order the Smart Key Maker from ebay. Did the trick - using the simple technique on another forum of just putting key in, plugging in device into port, turn on, take out, put new key in. Or some combination to that effect. Can dig out the reference if need be. This allowed the car to start with the key, and other key still worked. Success! Remote buttons still don't work.
3. Try the on/door open/close/open/close/key out/in trick, followed by the 'add key' option, and holding the remote lock/unlock buttons. Again, I can find the instructions if you need it. Took loads of tries, turns out I was holding the lock/unlock buttons for too long. Key now operates remote, ignition, and physical locks.
Toyotas seem to have at least 5 different procedures for both ignition and doors across their models. Getting the right info was a pain, with contradictory advice everywhere. The remote lock by door open/close procedure seems to be very common across models though.
Hope this helps