Hi Carlos,
It looks like jQuery does some "is this element in the document" checks before deciding to apply the animation.
However, ShadowDOM spec says that document.contains(someNodeInShadowRoot) should return false for encapsulation reasons.
Polymer's gesture library implements a "deepContains" method that works around the ShadowDOM limitation.
As a total hack, I tried setting jQuery.contains = PolymerGestures.deepContains, and that worked.
This is absolutely not supported, and I'm suprised it worked, but maybe you can use that for now.
I suspect that jQuery will have to implement something similar to support ShadowDOM's notion of contains sooner or later.