Fixed the error message on the Widget Permissions page in the next release. It occurs if there is a wiki-related widget that has not been assigned to at least 1 widget position. This is typical of widgets that were created solely for use by BB-Codes rather than for sidebar.
As for widgets not appearing intermittently, I have not noticed this issue on your site. However, I have noticed that some wiki areas seem to have no widgets assigned. If you are navigating back and forth between areas, this might give an impression of intermittent widgets.
For your "System" and "Test" areas, if you go into the AdminCP Area Manager's edit page for them, check Miscellaneous options > Widgets shown in this area.