I recently had to fight with an issue on a Windows 2012 Server with IIS 8, and a web site that kept on forcing the user to type in authentication credentials to access a PDF file located in a subdirectory.
I did the usual checks:
But to no avail. What stood out for me were:
Point 1 above suggested that something else was servicing that resource. Point 2 above suggested that it was not an NTFS permission issue.
Eventually I figured it out. This machine happened to have IIS and SQL Server with SSRS installed. SSRS naturally takes over the /Reports URL - I assumed that it would be overridden by an application bound to a subdomain. That was not the case. The /Reports got intercepted by SSRS and naturally it was set to Windows Authentication, which caused the prompt.
The solution here could either be to: