I have to disagree with you anonymous, sometimes (about 50% of the time?) the game will just end the moment the rat collects the last cheese. The end screen shows him in the start location of the bonus round, but it doesn't begin. I've been in the bonus round without all the letters and still got to play it (with less to collect), and I've finished with all the letters and a huge amount of time and not been allowed to play.
Worth noting; if you get to play the bonus round with all the letters, you can open the big door by knocking the two balls into their proper holes, right by it. Doing so gives you access, it seems, to extra cheese, but I don't know how MUCH extra yet....
The problem johnH is describing is a bug. I programmed the game and we never ran into this with our beta test. Of course we beta tested with only 12 people over 1 week. Since we released the game yesterday, we've had thousands of plays and it has served to be a much better Beta test than we could have imagined! I think i fixed the bug and will upload a new version soon. The problem is, the buggy version (1.0) will continue to proliferate around the net with the new version (1.1). Such is the nature of free web games....