solved. I have also acrobat installed beside adobe reader. I change the .pdf connection (control pannel->Programs ->default programs) to acrobat, then it works.
Firstly I got the upgrade to 4.0.1, although had to do this from the website rather than from within EndNote.
Then, when I tried to attach a reference I unchecked the box “copy this file to the default attachment folder and create a relative link”
When I didn’t have this box checked, I was able to open an attached pdf. Funny thing is, now the box is checked again and I am therefore using the copy function, it still works. Problem completely solved.
So in summary, upgrade, then experiment with checking and unchecking that box.
The following is what I found on endnote website and it works for me.
EndNote: Troubleshooting launching new PDF attachmentsIf EndNote is unable to launch newly linked PDF attachments within EndNote library records, there may be a problem with the versions of Adobe Acrobat installed on your computer. To verify the cause of this behavior, download another PDF reader. Click the following link, and download “Foxit Reader - Free”. After installing Foxit, double click on a PDF outside of EndNote to make certain Foxit has been set as the default PDF reader. Then try creating and opening a new PDF file attachment within an EndNote library record to see this resolves the problem.
I can now open most of my attachments, except for those with long file names.
I had the same problem after I upgraded to a new Mac. I found that the files were not being copied to the PDF directory (even though EndNote appeared to be importing them just fine). I ended up changing the permissions on the EndNoteLibrary.Data directory, and applied those permissions to all enclosed items. This worked for me.