I have been having this problem since I upgraded to Leopard. When adding references/files to the library, EndNote X1 crashes when it exits. If no changes to the library are made, no problem.
The issue is 100% consistent, I have the problem on my iMac and on my Macbook Air. Both access the same libraries from an iDisk.
I had the same problem with X1. I’ve now upgraded to X2 after acting as a beta tester for the upgrade and the problem still persists. I reported the problem to Thomson througout the testing process, but it was not resolved. Perhaps it will be fixed in the upcoming patch for X2.
This appears to be an issue with the way in which Endnote interacts with the idisk (essentially a webdav disk).