Endnote is likely a big part of the problem. It's very bloaty, and the newer versions only seem to make this worse. Here on MacRumors they had a software special one day for a program called BookEnds, an OS X resource manager. I figured I'd give it a shot, and now I can't imagine using anything else. It's cheaper than EndNote and works with Word 2004/2008 and has all the features you'd expect. I had some issues with making citation style for my PhD (my Uni is very specific) and their tech support by email was fast and actually helpful. And no, I don't work for them, I just thought I'd share my extremely positive experience with the software.