At work we setup a Twiki, and Internet Explorer refused to send the NTLM authentication, instead it showed a login popup. The problem was that our Windows domain, say mycompany.com was different from the Twiki URL, which was othercompany.com.
The solution is to tell IE that othercompany.com is a trusted site. ‘Tools’ -> ‘Internet Options’ -> ‘Security’ -> ‘Local Intranet’ -> ‘Sites’ -> ‘Advanced’ and add it in there, this must start with http:// or https://
The problem and solution are explained here:
Apache::AuthCookieNTLM – NTLM (Windows domain) authentication with cookies
Note that this will be a problem not just with that Perl module, but with any cross-domain NTLM authentication. IE correctly refuses to give out your username as it doesn’t know it can trust the site.