Ah... well what should I change then? Should I go to manage SEF Urls and change them in all of the instances of that url ?

Well two are from custom html modules, one is from a most read articles module. There is a menu item linking to the article as well, but the menu is unpublished (so I could control module positions within those articles)

The custom html modules contain the full link, index.php?option=com_content&id=198&itemid=145, or something like that. Should it just be index.php?itemid=145?

Hello!
No the url is not the same as an existing file. I'm not sure exactly why it is different. I think maybe it has something to do with the fact that there are three links to the same article coming from the home page? Would that cause a problem?

There are only two articles in that section and the other one shows up perfectly.

I have links to articles in the footer (the usual terms of use, about us, contact, etc). One of the articles brings up an internal server error. Only one of them though. Everything else on the site works, including jomsocial, kunena, hwdvideoshare and everything else. So far I have not found one broken link (though some generate unwanted strings, which I will edit out later), with the exception of that one broken article link. It doesn't matter where it links from either, the most read articles module when published includes a link to it, and it is broken as well.

This is my first experience with JoomSEF, as the internal Joomla sef has usually met my needs with other projects, so I'm not sure what is causing this problem. I know that I have configured my .htaccess file correctly, as everything else is working fine.

What could be causing this problem?