You're right, I've never heard of backward compatibility that didn't work flawlessly. I know very little of Java, but if the backward compatibility isn't perfect then I could understand why companies would be hesitant to upgrade.
the java bytecodes remain unchanged from jvm 5 to 6. The bytecode is all the jvm sees. Thus the backward compatibility does work almost perfectly. Also jvm 6 has been out for long enough now to have ironed out any potential issues if there existed any in the first place.
There have been regressions over the years. Just because it is intended to be backward compatible doesn't mean there aren't occasional bugs that can break an application running on top of the JVM.