What do you mean "are not being rewritten"? The link takes you to /login and not /index.php?main_page=login - or did you hard code the links?
It seems like you should reset SSU cache. I think you're mixing it's cache from two different shops since you obviously have some URLs with cPath showing and some without (your dev site probably doesn't have Alias turned on). Anyway, try resetting SSU cache first. If that doesn't do the trick, set SSU status to false and remove the .htaccess file from the root (or rename it to htaccess.old) and try again. It seems you're simply missing something because SSU works fine: