Susan,
The plugins are below. I am not sure if these are the items causing the problem. I am thinking it is the .htaccess file. Any ideas?
OnBeforeManagerLogin
Forgot Manager Login
OnDocFormPrerender
ManagerManager
Quick Manager+
OnDocFormRender
ManagerManager
accessresource1.0
OnDocFormSave
Quick Manager+
OnInterfaceSettingsRender
TinyMCE Rich Text Editor
OnManagerAuthentication
Forgot Manager Login
OnManagerLoginFormRender
Forgot Manager Login
OnManagerLogout
Quick Manager+
OnParseDocument
Quick Manager+
PHx
OnPluginFormRender
ManagerManager
OnRichTextEditorInit
TinyMCE Rich Text Editor
OnRichTextEditorRegister
TinyMCE Rich Text Editor
OnStripAlias
TransAlias
OnTVFormRender
ManagerManager
OnWebPageInit
Subsites
OnWebPagePrerender
Quick Manager+
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The .htaccess file only rewrites incoming URLs before feeding them to MODx. It has nothing at all to do with the URLs MODx generates.
Most likely it's either subsites or multisite. Make sure your site is configured properly to use them, and they are configured properly.