Have you adjusted EndNote’s “Find Full Text” settings to maximize results per the KnowledgeBase (reproduced below as shortcut URL http://endnote.com/kb/82212 doesn’t seem to be working):
EndNote: Optimizing Find Full Text results with X2 and later
EndNote X2 and later can automatically locate and download full text files by accessing several sources, including: DOI (Digital Object Identifier), PubMed LinkOut, and ISI Web of Knowledge Full Text Links. EndNote will try to use all of these methods to optimize the likelihood of finding full text files associated with your bibliographic records.
The ISI Web of Knowledge free journal set is checked for all users; subscribers may have full IP-based access to all resources. In cases where full text PDF files require a subscription, and you or your institution have the appropriate access, EndNote will attempt to authenticate and automatically download the appropriate files. If EndNote cannot find the full text file, it will often be able to attach the URL of the provider’s Web page for the article for easier future access.
To optimize your chances for getting a full pdf file, make sure you are set up to use your institution’s subscription databases before running “Find Full Text”.
Additional resources will be added dynamically to the search process based on your feedback. To suggest a source be included in the find full text option, use the Product Suggestion Forum page.
EndNote X3 and later additional information:
In EndNote X3 and later it is possible to authenticate and use your institutions OpenURL server.
To do this, on Windows, go to the Edit menu and choose Preferences. On a Mac, go to the EndNote menu and choose Preferences.
Go to the “Find Full Text” option here, and check the resources you want to use.
If your institution has an Open URL server, put that in the “OpenURL” box.
If your institution has a login page for access to restricted databases, put that in the “Authenticate with URL” box.
If you entered anything in the Authenticate with URL box, before going to “References->Find Full Text->Find Full Text…” choose “References->Find Full Text->Authenticate.”
You may also need to use this command to re-establish your connection to a subscription database.
Your institution may sever your OpenURL connection after a certain amount of idle time. Unfortunately, there is no indication when that happens. You will need to go to the “References->Find Full Text->Authenticate” to restore access to the site.
Just selecting “References->Find Full Text->Find Full Text…” during this EndNote session will not restore authentication.