Read this article for things you can check if you find that EndNote and Word won't play nicely together, and ways to fix this. And/or watch a video from the EndNote company with more settings to check and fix.
For more on using EndNote with a Mac, look at this article and follow links from there for more.
For more on software compatibility, look at this article.
If you use EndNote with Pages, look at this article (scroll down for Pages 09).
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WATCH THE VIDEO