ASP.NET Security Puzzle -- Need Explanation

I've got an ASP.NET website that has several IIS sub-applications running on it.  Some of the sub-apps have authentication=None and were always working fine.  I recently changed the root app to have authentication=Forms, with authorization denying anonymous users.  Several tests since that time have always shown the sub-apps still working, as expected since they are separate applications in IIS and ASP.NET.  Now all of a sudden, with no difference that I know of, one of these sub-apps started popping up the Windows Integrated Security dialog.  Looking in IIS showed that anonymous access was still granted on the folders and files of this app.  I also verified that the security permissions for all users were identical with this app and ones still working.  I changed the root app back to what it was, and that didn't fix anything, but I didn't expect it too anyhow.  Somewhere along the way in my checking, one of the other sub-apps also started having this behavior.  I don't know of anything I changed that could possibly have this behavior right in front of my very eyes!  I couldn't figure out any explanation, and therefore no fix, since the only way I know for this dialog to pop up is either anonymous denied in IIS or file/folder security settings.  My colleague finally took a web.config file from one of the working sub-apps and put it in one of the non-working apps -- and it worked!  The only difference we could find between the web.config files was that the non-working app did not have an authorization section.  Of course, it also had authentication=None, and anonymous users were allowed in IIS, so I don't see how this could matter.  We looked at the other non-working app's web.config and it was also missing the authorization section, so we added it -- and it worked too!  By the way, this authorization section simply says to allow authenticated users -- it does not even mention anonymous users.  Even if the app root were affecting this, it also allowed authenticated users except in one unrelated sub-folder, so again I don't see how this change really could help.  I've since tried removing authorization sections on a few of my local web apps and it has yet to make any difference.  Also, to the best of my knowledge, nothing in the first sub-app changed, and I know the other one quit working right before my eyes, again not touching it since it was the other one that was being checked.  I still cannot fathom why adding an authorization section, especially one that does not even mention anonymous users, could make a difference.  Anyone know of an explanation, or some other things that I should look out for that could cause the Windows login dialog to popup?

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