I am seeing a similar situation. I was getting %BEG_OF_TITLE%Most Popular Articles%END_OF_TITLE%, but I had a Popularity Contest plugin. All but two of the plugins in my second sidebar disappeared, along with the Save Changes button. Up until I tried adding a text (php) widget, it worked well. Now it says that I’m still using the widgets, but they do not appear in the widget admin area, nor on my site.
I have tried disabling all Popularity Contest plugins, but the problem remains.
