I have had a very similar problem (not absolutely identical) with X8 and … the solution which we arrived at could also address similar issues. What caused my problem was importing a style not a reference, but I think this is a close enough issue to that described above and had the same error report on screen.
After going through exercise of copying the data folder and creating a new primary .enl file I had a the above error report. So, after uninstalling and reinstalling Endnote three times (which regrettably I am a past master at! – heed the warning from TR… back up your Endnote files often!!! Every time you add something to the library is a very good idea.) with various versions; and an hour or so with my University’s help desk’s most experienced Endnote user (Simon has been using it since version 3, 15 versions ago!), we ended up resolving the problem.
What appears to be occurring is that when Endnote is importing it minimises the active window for the active .enl file, such that you can’t see it or find the active window either within Endnote or Windows. By copying the original folders and files into new files and folders (a copied data folder of the original folder and a new ‘file.enl’ created in Notepad) then importing (not using the Recover Library function – although this could also work) from the original .enl file, then clicking on the W indow tab in Endnote and selecting Tile Vertically , hey presto… the desired .enl file displayed on the screen, with the imported references that appear to have caused the problem added in. (The cause may be a range of things ranging from poor coding to a dodgy API or some other challnge from the cosmos with the latest version X8).
I hope this helps others!
John Noonan
Curtin University
Western Australia