I have used this plugin for a long time--almost a year, and it never broke before. Since the new developers took it over, however, my sidebars just disappear--as in vanish into thin air. My primary sidebar is gone..and my footer sidebar has disappeared three times. The custom sidebars are sometimes there and sometimes not. Looking at the forum it appears that this issue is happening very frequently over the past few weeks or more to other users as well, and the developers have been silent about the problem depite many requests for help.
It's really too bad that such a good plugin has been left to fall apart.