[eluser]jedd[/eluser]
Hi mshaw087 and welcome to the CI forums.
You have indeed painted an interesting picture here.
Can you please clarify - if you use any address that involves a route, and you are using FF, does it work as anticipated?
It seems a curious (read a tad unlikely) combination of server and browser side interactions here .. as the route, controller, and various other things are all happening up on the server.
My first guess would be that you authorised yourself using your IE instance, and it has retained the password. You can either try to flush cookies, memories of passwords/forms etc, or perhaps just try hitting the URL from a different machine - to really prove this out one way or the other.
When you say that MY_Controller constructor is not run - how are you ascertaining this - some echo statements, or the presence of some variables elsewhere?