Just in case anyone runs into the same issue that I did, in the instance where Omeka is not at the site root, You need to add the following to your .htaccess files:
in /.htaccess:
RewriteBase /pathtoyourinstall
in /admin/.haccess:
RewriteBase /pathtoyourinstall/admin
This refers to the external path path that users see. So, if your install is at www.omekasite.org/omeka, it would be RewriteBase /omeka.