Hi
I am having exactly the same problem, with the same OSX version. X6 and X6.0.1 index @4000 entries of a 5000 pdf library from X4.0.2 and crash. I stayed away from X5 because of the same problem, and X4 gave me the same result before the 4.0.2 patch.
Not much help from Thomson Reuters ’ you must have a corrupted library or pdf". I tried repairing the library and exporting it as .enlp with exactly the same result on reimporting. Because I had the identical issue with X4 before the X4.0.2 patch, I think this is an Endnote bug / inability to import large pdf libraries. I am trying to export my Endnote library to another reference manager software as the only current solution to get away from this and the OSX 10.8.2 cache bug,