index.php and .htaccess are in the main section: http://www.???.com/
So .htaccess & permalinks work, I can manually copy the text into .htaccess. However, WordPress will not automatically update it (patricularly annoying when adding/changing pages). I have tried setting .htaccess to 666 or 777, but neither work. I don't think its an issue like AllowOverride, since .htacess works, but WordPress just won't update it.