It seems like the function
is_active_sidebar() has gone from the MultipleSidebars class, in favor of using
I think that change deserves a note in the changelog. There are references in the readme.txt but you only see that file AFTER the upgrade.
There are themes that depends on calling
$MultipleSidebars->is_active_sidebar()which used to be a public function (ver. 1.2.3 at least). They have to be rewritten to suit the new format and it's a bit late to find out, when the menu system is broken.
Apart from that - it's a great plugin!