I’ve had this problem for years, and I think I’ve finally fixed it.
It turns out I had a Styles folder in My Documents containing duplicates of every Style file in Program Files. I deleted all the duplicate Style files in the My Documents folder (thousands of them) and Endnote and Word now seem to be behaving.
I suggest looking for another Style folder on your system and making sure there are no duplicates. The same might go for Filters and Connections, although I didn’t have any of those in My Documents.
This may not be the cause for everyone, but I hope it helps someone.