This one is pretty strange. I’ll install a fresh copy of 1.4.1 and 1.5.0.1 on an IIS server, and change the base url in the config like normal. I then create a new controller and view.
I try to add a link to the new controller on the welcome_message view as a test, and when I click it, it just reloads the welcome index controller. I’ll also try to type in the full url (like http://www.mysite.com/ciDirectory/index.php/testController) and it does the same thing (http://www.mysite.com/ciDirectory/ shows up in the browser, but http://www.mysite.com/ciDirectory/index.php/testController is now in the url field of my browser).

I am not sure what’s going on, but 1.3.3 works just fine. I hadn’t noticed this bug since I didn’t need IIS until now.

Hope someone can pinpoint the discrepancy between 1.3.3 and 1.4 and higher.
Thanks!

Look in the troubleshooting page of the user guide.  IIs servers do not support the PATH_INFO variable necessary to run clean URLs.  You’ll need to add a question mark, as per the user guide.