Thanks for the reply. The issue is that if someone adds a piece of content and clicks "save draft" they get a message back saying that the content has been saved. However, when you try to look for the content object (either in the folder where it was placed or by search) you can't find it.
We did run all the upgrade scripts and they appeared to complete successfully. Those SiteAccessSettings settings were originally in site.ini.append.php. I repeated them in content.ini.append.php just in case.
Seth, this is expected behaviour. You can read more about "Store draft" button here: http://ez.no/doc/ez_publish/user_manual/3_8/the_administration_interface/the_object_edit_interface
As long as object was not published then you can't access it in the content tree. You can save draft using "Store and exit" button. Your saved drafts you can find in your My account tab.