We have an internal web site that is https only and that prompts for login with an "authentication required" popup. This works fine for internal users. However, when I try to access it via the web resource I've defined, I get an error saying "Cannot establish a secure connection to the URL. Check if this connection requires http instead of https, etc etc"
Is there a setting I can change that will allow the popup dialog box to be displayed?
You wont exactly get a pop-up window rather you should get a web page which lets you enter username/password.
This is called the IVE intermediation page, if the https server is requesting for authentication, the IVE should send you the intermediation page.
Ensure that you have ACL's configured on the IVE for the backend web server.
One thing to check is your required encryption strength. If you only allow connections from 128bit browsers, and deny connection that use less than this strength, you will be unable to connect to an internal HTTPS resource that uses less than 128bit encryption because the IVE doesn't differentiate user connections, and connections it makes on users behalf.