The latest update for Plus! also silently changes the compatibility settings for Messenger back to normal if you've set them differently. I find this a bit strange, since it's a setting I've made consciously and on purpose. If Plus! thinks it knows better than me, I'd like it to tell me why it does so (and, perhaps, even ask for my permission to change a setting).
The reason I changed it is that I like my taskbar with one button per window. This is a nice and supported option for Windows 7, but Messenger is a douche and wants an extra button for my avatar, and thinks that makes up for having no tray icon. Since I respectfully disagree, I made it think I used Vista.
Perhaps there is a possibility, if compatibility mode is unhealthy for Messenger, to change its behaviour with Plus? For example, the jumplist could perhaps be customizable, and the strange avatar-nonwindow might be removable
By the way, I'd welcome a bit of info about what exactly is so bad about compatibility mode (I've seen Patchou warn against it here and there). It seems to work just fine for me, excepting the jumplist.