Based on the error your SSIs are throwing up, it could very well be that your password protection has caused this to happen (note that you can get 500 errors with errors in your htaccess instead of the standard 403). Is anything that you are running trying to access a directory that contains the htaccess/htpasswd file (if your htpasswd file is in any web accessible directories, I'm going to hurt you

)?
Easy way is to rename your htaccess to bak.htaccess and run something and see what happens...I'm not saying this is definitely the root of your problem, just the possibility. And if your host is upgrading something, you should have gotten some type of notice from them (if they were a host that realized they worked for you), but you should definitely contact them, as has been pointed out.