I keep running into licensing conflicts when developing locally, what is the recommended way for doing this?
If it is an enterprise site, ask in the comments for an enterprise developer license when you order a new license.
Try an iisreset after you've stopped the other ones. I misunderstood your question at first.
I like using this XP Pro IIS Admin for switching between sites. You can get it here: http://www.jetstat.com/iisadmin/
I've never had that problem while using XP Pro IIS Admin.