If you're having an issue after updating, we would advise double-checking the points below. With a large customer base, anytime we update a product, there are tens of thousands of people updated from many different versions.
A well thought out system called USE flags complement this system well.
The Google Plugin for Eclipse periodically checks for updates to the plugin and bundled SDKs.
When updates are available, the Google Updates Available... If you do not want to be notified of updates to the plugin, you can disable them by selecting the Google page from within the Eclipse preferences dialog (which can be accessed via Window Preferences if you are on Mac OS X).
Rather than having to tinker around with every program you compile, you can set some global USE flags.
Most packages will take note and your system will be made into one harmonious whole of software agreeing with each other about what should be used and what should not.