When building projects after installing JDK 1.6, you may get build failures complaining about /System/Library/Java/Extensions/AppleScriptEngine.jar targeting a 1.6 Runtime. This jar gets replaced by the 1.6 install with a version that is not compatible with the 1.5 JDK.

If you are not using this, you can remove it from the jars included in the System JRE for Eclipse builds.

Go to Eclipse - Preferences and search for "Installed":

Edit the default, and select the AppleScriptEngine.jar:

Click Remove and then rebuild your projects.