Thanks for the detailed feedback! Responses below:
Re: start over message, yes, that's true. I'm not sure I want to modify the messaging though, just to make sure people know what they're getting when the choose to restart the puzzle.
Re: losing clue progress on a saved puzzle - also true, good catch. It probably won't be included in this launch, but I'm making a note to eventually figure out a way to save clue states as well as grid states. Thanks!
Re: beta stats, I am probably going to dump user/puzzle stats acquired during the beta phase once we launch the site - that way we won't have skewed numbers based on people testing for bugs, and everyone can start acquiring stats on their accounts at the same time.
Re: invalid puzzle size... I think this should be fixed now. I suspect this is happening because your browser has saved the "init2.php" page and you are somehow navigating directly to it, bypassing "init.php". Now, if that happens, instead of failing completely as it was doing for you, the page will have two fall-backs - first it will check for your last-used grid size preferences via cookies and use that, and if it still has nothing at that point, it will then default to a 4x5 puzzle.
Thanks again for the feedback!