I doubt if that (forced HTML5) is a IE-9 specific issue. But it might be more noticed in IE-9 since there is more ways to disable or otherwise "mess up" the Flash Player in IE-9 than any other browser I have encountered.
It looks to me like on any HTML5 capable browser, if Flash is not installed or is installed but blocked or disabled, then HTML5 will load automatically, regardless of the state of Opt-in/out and in fact independant of browser cookies altogether. That's been the case on the new style YT channel page Featured Video for quite some time, but it also now seems to be the case on YT Watch pages when the given video is available in an HTML5 compatable format, and there is nothing can be cone about it other than to ensure that Flash is installed and also enabled and not blocked on the given browser. And to beat around the bush with IE-9 ..... IE-9 can be set to copmatability mode of IE-8- and when that is done, IE-9 is not HTML5 compatable - hence you would likely thenget a message that Flash needs to be updated - meaning that Flash is either not installed, or is installed but disabled or blocked.