for some odd reason quicktime, or for that matter all movies are not working in safari for me. it coincides with me recently using firefox a bit more than i used to, i don't know if that has anything to do with it.
Maybe start by resetting Safari from the Safari menu. If that does nothing, then try dragging a file named com.apple.quicktime.plugin.preferences.plist to the Desktop.
Just to be clear, are you saying Windows Media Player isn't recognising WMVs? 🙂