Apple has posted a fix to the Apple-Java mailing list. Here is the post :
Hello Java developers,
As of 10:00AM PST today, Apple has revised the "Java for OS X 2013-004" and "Java for Mac OS X 10.6 Update 16" updates to fix a widely reported issue with the original updates that shipped to customers on Tuesday.
The crux of the problem involved dispatching events through sun.awt.AppContexts which were setup incorrectly when the JVM first initialized the AWT. Some impacted applications could work around the problem by changing the order of initialization of these classes, but we believe that we have provided a comprehensive fix with these revised updates.
If you have previously installed the xM4508 versions of these updates you can upgrade to the fixed xM4509 version by manually installing:
support.apple.com/…/DL1572 (10.7, 10.8+)
You can check if you have installed the xM4508 versions by running:
/usr/libexec/java_home -v 1.6 -exec java -version
If you have not installed "Java for OS X 2013-004" or "Java for Mac OS X 10.6 Update 16" already, you should receive this fix automatically through Software Update / App Store.
If you have installed the previous Developer Package, we have posted fixed versions at:
We apologize for the inconvenience this has caused, and would like to thank all of the developers who have brought this issue to our attention.