Somehow, someone (according to my logs and IP matching, The Ultimate Koopa) managed to run one of the old new-files scripts this morning, and the old first page (index.html) has a higher priority than the new page (index.php).
The old script can't be run anymore... I thought I'd fixed that once, but I guess not.
P.S. Poking random scripts that are returned to you when type in an incorrect URL usually isn't a good idea.