I now only have to switch theme and back to lose the top menu widget. That is without disabling the plugin as described in my first post.
WP 3.8.1 and gantry 4.1.1
I can provide a testsite login for gantry theme authors for a quick check.
EDIT: this behaviour seems to only occur when addthis(3.5.8) is active. Plugin doesn't seem to work with gantry anyway, but still indicates a problem that should be fixed.