I had issues with updating Eclipse itself. The last time I used Eclipse was when I updated the main IDE itself. The update somehow broke my plugins (including Google's ADT) so badly that I had to remove Eclipse and reinstall it and the plugins from scratch. I decided to move on to IntelliJ after that, and I have not had any update issues since then.

This was back in the Eclipse 3.5-3.7 days, but with 4.x already out, it's possible that this issue has already been fixed.