r20212 introduced new methods for registering custom headers and custom backgrounds. Everything now wraps add_theme_support(), and the various HEADER_ and BACKGROUND_ constants are gone.
This is ideally backwards compatible (I am cautiously optimistic), but because of the many factors at play here — child theme inheritance, constants, and theme support — it is very difficult to test.
I am going to come up with some sort of a testing protocol in the hope that we can crowd-source testing the WP.com themes that implement custom headers or backgrounds. For now at least, if you are running a theme with custom header or background support, please test and make sure functionality did not change.