No WPMU plugins working in mu-plugins folder

We recently looked to install some of the plugins including default theme. The plugin was first place into the plugins directory by mistake. It actually appeared to run. However, when we removed it and place the plugin into mu-plugins folder, the plugin does not work. Any idea? does something get set in the database when it is installed in the normal plugins folder? We need help!!! we are already having folks sign up and we cannot get TOS or default theme to work..