Is there a way to stop the Flash?.. well.. put the two versions on separate pages. I thinks it’s confusing and a little counter productive to be displaying the same thing (is it the same home?) in two different player on the same page. Especially since one is “below the fold” so to speak. Display a primary video, then offer the option to view it in a Windows format, if you like. Of course, after the 95% of viewers with Flash players watch it, why would they want to switch to the Windows version? If you did choose to present two Flash players on the same page, it would be much easier to have the two of them talk to each other, than having a WMP and a Flash player share controls.
I think the video used in the WMP is a better intro than the Flash Panorama. Convert the .wmv to a .flv and play it as the first video. Then allow users to click to the Panorama view. Not being much of a “back-button person myself, I would have the images open in a pop-up or something (target="_blank") instead.
Eye for Video