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I have found the issue, it currently does not change the state of the checkboxes to checked when all sub items should be checked. The order should be down to top and currently it follows the DOM order. A quick fix for you could be checking the tri-state checkboxes (not the deepest level) yourself.
Furthemore, I will try to solve it, than the issue #3 will also be solved.
On three level tree, top item loading in tri-state when all subsub items are checked
http://jsfiddle.net/rNL8X/1/
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