The latest IE patch removed support for authentication-in-URLs, so user:password@site.com doesn't work. Which, if you ask me, is an inconvenience, but necessary, seeing as how many people were being conned through various manipulations of that standard.
As for passing it through to neomail, I can't help you. Have you tried replicating the form Neomail uses to get the username/password? If you copy the form's logical structure (the form/input tags, etc.) and make sure the target is accurate, it might be possible to change the user's login screen that way.
Let me know if I'm off the mark with what you want to do!
dave