This is a serious problem for the WDTV product line. It needs to be addressed quickly before the problem starts to grow, as more people start using the new versions of mkv authoring programs, many of which are (based on) mkvtools.
It took a lot of troubleshooting and research to figure out why I suddenly had no audio on files I just created. MkvMerge now defaults to using this header compression feature, and you have to manually change the option to NO every time you use the program, otherwise the created file is incompatible with the WDTV players, at their latest (current) firmware levels.
This "new" feature is based on an existing mkv spec, but it just wasn't used much before. Now that its being used then the WDTV needs to properly support it, by following the existing spec.