If you are working with Java on OS X, then you are probably aware of 13949712720901ForOSX, a call for Apple to support Java 6 on Mac OS X Leopard.
My personal take on this (stressing the personal - despite my highly exalted position at Sun I have no insider knowledge) is that Java 6 was in Leopard at some point in time (witness the Java 6 developer preview download at ADC - long gone now). Apple put resources into iPhone at the expense of Leopard. I reckon that Java 6 was cut to bring in Leopard's ship date, and Java 5 hastily put in its place, hence the Java 5 issues we are seeing.
All of this would be of little import, were Apple not dealing with a developer community that has become addicted to openness. Apple's ruthless, consumer-oriented, information management just doesn't work with this crowd. And, devoid of any official position from Apple, the community assumes the worst. It's only a matter of time before the first blog entry appears alleging that Java 6 was dropped from Leopard because Steve Jobs spends too much time eating babies (oops - there it is! ).
I guess the first we'll hear from Apple is when the download appears in Software Update. It can't happen too soon...