There is actually a setting stored inside the shell container, for example AVI, which tells it what default screen format to use. See My ConvertXtoDVD example. I suspect that you may have that set incorrectly when you re-encoded your videos.
Unfortunately I'm not sure if you can force WMP to a different AR (I ran a search but couldn't find a way). So what you may want to do is check your settings and, most likely, re-encode. Or, of course, use VLC where AR is easily adjusted, as you well know.