Is there a known problem by making Endnote work in Mathematica 10.1.?
There seems to be connection since Endnote is opened from within Mathematica, but it is not possible to find any references in the small dialog box.
Are you using Windows?
In my experience, there aren't enough people using this feature to probably get help on the forums. I would contact Wolfram Technical Support about this issue. https://www.wolfram.com/support/contact/
Let them know a bit about your computer (it's operating sytem for example) and what your activation key is ($ActivationKey)