I've just released JB Library v2.1 which features two new improvements to the way that the library plugin works.
A new script loader
Technically, jQuery should be able to load as many times as you want on a page - although best practice is to only load one. Even with multiple instances of the jQuery library loading on the page, it's core functionality should remain unaffected. However because Joomla components, modules and plugins are triggered at different times during a page render and because there are a few different ways to include assets within that rendering, it's not always possible to control the exact order that scripts are loaded on the page and so we often end up with a jQuery conflict.