I ran into this same issue.
What is mostly likely occuring here is that each of your 50 redirect sites has the same directory configured. In IIS7 when you setup a redirect it is stored in web.config in the site directory. Since all 50 sites share the same directory when you change one, you change them all.
My Quick solution was to create a separate directory for each of the redirection sites so that each has it's own web.config to store the redirection settings.
My longer term solution was to build a single a Database driven redirection site. It catches all of the traffic not already assigned to a site, looks up the URL in a DB, then redirect appropriately. It was some simple code.
-Phil