Okay, as it turns out, you need to modify the value HKEY_CURRENT_USER\Software\Microsoft\Office\12.0\Access\Access Connectivity Engine\Engines\SystemDB
to "%appdata%\Microsoft\Access\System.mdw"
Or, in the case of Office 2010, HKEY_CURRENT_USER\Software\Microsoft\Office\14.0\Access\Access Connectivity Engine\Engines\SystemDB
Not sure why I didn't look in the registry first.