I’ve been going nuts trying to figure out why calls to the Multi-level Navigation script appear multiple times on one site. I think I’ve nailed it down to two specific plugins, whose deactivation solves the problem, and now produces a clean output:
Yes, you understood correctly: that’s exactly what they did… Weird indeed. There’s a remote possibility that there are other plugins that interact with those two, exacerbating or fatally triggering that, um, feature – but I can positively say that those two are responsible for causing appearances in multiple places of bits of your plugin, in the HTML head section.