When running in non-embedded mode I cannot close any plugin window

It's not a bug, it's a feature. The NPAPI used by Silverlight does not define the possibility for a plugin to shutdown itself, only the browser can do this. If we would allow you to close the window, this would result in an undefined behavior (the sound of a video continues, although the window is closed, ....). This is the reason why you cannot close it, but you can still resize or minimize it.