Hi
I had the same problem and I fortunately succeeded to solve it by going through these steps:
- I changed the " User Account Control" to the lowest level ( Never Notify ) by going to " Control Panel\All Control Panel Items\Security and Maintenance" then clicking on " Change User Account Control Settings" on the left
- then I changed " Compatibility Mode" for " Endnote.exe" file in the " EndNote Properties" window to " Windows 8"
- and also went to the " Security tab" in that window and changed " Permissions" for every single " groups and user names" to " Allow" " Full Control"
***unlike some comments I had no need to check the " Run this Program as administrator" option***
***and I did nothing to the MS Office or Word application ***
***forgot to mention that I am running Endnote X9 and MS Office 2016 on a 64bit Windows 10 ***
I hope these steps will work for you too