The biggest issue I run into with plugins and backbone is ones that rely on jquery position. The position api needs to be called after the element is attached to the dom and is not hidden. I like to encapsulate all the view logic within the view, but nothing alerts you to when the element has been attached and is no longer hidden. Typically I'll fire off an event in the router or parent view to then enable the plugin.
quickly looking at the bootstrap javascript they are making calls to $().offset which also doesn't work for hidden elements, so yes were talking about the same thing.